Ok so without giving stuff away I will try to give a rough beginers guide without spoiling anything but the features of the game as the learning curve can be somewhat daunting.
For the Ultimate Guide, simple ask questions on the X3:TC forums. You are guarenteed a quick and honest response, unlike the majority of gaming forums.
Ship Controls Default - The new default one which uses right mouse fire, left mouse or space to fly. This however only uses manual firing and not bore sight firing which you need to use for auto-aim when you purchase flight command software I. I insist you do this first and then bind right click fire to bore sight fire.
Ship Controls Classic - My prefered method is rebinding the controls, right mouse to Classic Mode, inverted mouse and left mouse as bore sight fire.
k key - This cycles through your flight command settings, auto-aim (red/blue flashing), normal guide (red marker trailing target), nothing (hardcore, good luck hitting 400+m/s ships)
Basic Combat - W,A,S,D These are your friends, just like in FPS games strafing is king. Keep to a simple clockwise motion 3 seconds on each key and you will soon dodge the slow HEPT gunfire (green stuff :P). Of course if they have beam weapons like khaak this doesn't work so well as they pew pew you.
Nearest Target/Cycle Enemies - Shift+T OR Home OR End will give you the nearest target to your ship, this can also be a missile which are very simple to shoot down if you follow the reticle.
Active Guidance - This helps you track the current mission you are one by highlighting the object your want with yellow brackets. To activate it press P then My Missions (enter) and select the mission you want guidance on by clicking on it and selecting Activate Guidance.
GOD - This is what players refer to as the Game Engine Economy self healing itself. Sooner or later you will find a Xenon/Khaak Invasion has settled itself into a zone and cleared it out of all Stations leaving a mass of debris. When these are killed off or moved on their way the Game Engine will respawn stations over time and the trading stations etc. This will also happen with Asteroids.
j key - This is your friend, this sets SETA speed, basically 6x faster than normal, you can go higher upto 10x however your PC may say **** you or if in a fast ship 300+ m/s you may well crash into an asteroid while your PC is saying **** you I cant process all this
Basic Navigation - Hit the . key and you will see a sector map, hit the , key and you get a universe map. On the sector map you see a radius around your ship (if in space). Terran start you have a duplex scanner which is a smal range radius, buying a Triplex scanner will increase this a lot. This is your eyes on the universe and is essential early on to uncover new stations and gates.
Gates - These are generally easy to find, they will mostly be on the N E S W access on the grid. Sometimes they will be visible, sometimes not so much and sometimes hidden cunningly behind an asteroid.
shift+J key - Jumpdrive. Essential item to purchase for your ship, however only available in a few places. This requires energy to jump however, 5 per sector but space is big, I think X3:TC is 120 sectors.
Starting Ship - This is generally pretty bad, a basic model of an M4 (if Terran Start). This is a light fighter, something thats not meant to take on big ships as you've weak shields and guns. However flown correctly you can take down an M6 if it does not have a rear gun.
The Terran Hate Me? - The Terran start is an odd one, they just don't like you snooping about. Best to wait until the plot tells you to go somewhere in Terran space before looking yourself else you'll be shot. Maybe Stalin won the war in this universe?
Everyone Hates Me? - Maybe your shooting anything that moves. The whole game is reputation based. Press P and p again, here you can see your titles which tells you what each race you've discovered think of you. These also unlock different starts. eg. 100% hated by all unlocks khaak (used to).
Autopilot Docking - While this is lazy mode it sometimes goes a bit wrong. Especially if your docking at a large solar plant it has a tendancy to slam you into the solar panels, so best to keep watch
Claiming Ships - Ok so your in combat shooting the crap out of that pirate and the ship turns red to blue STOP FIRING! This means the pilot has bailed out and you can now capture that ship. To do this fly slowly upto it (get real close) and hit shift+e this will eject you from your ship putting you in a space suit. Fly close to the ship, target and Claim. Then jump back in your own ship. Simply return the ship to a ship yard and repair or sell, upto you. Later on you can buy System Overide Software, this claims a ship but from a 5k range without you needing to eject.
How to Change Ship - So you've claimed or been given a new ship, there's a few ways to switch ships. The first obvious one is if you're claiming one then press Shift-E and you will enter the ship targeted if in range. Another method is have both ships docked at the same station and select Advanced -> Change Ship. Another method later on is using the Transport Device available for purchase which can beam you between ships within a certain range.
How to transfer freight - So you own a few ships and have that 1 Jumpdrive that cost you a lot. Simply dock both ships and go to Advanced -> Freight Exchange. Then shift the freight left/right between the ships. An alternative method to this is to use a Transport Device which costs 56k and allows freight movement at a limited range without docking. A third method is to use a Player HQ or Warehouse however I'm not sure these made the move to TC yet.
Repair Laser! - So this is new to X, basically you can eject in some safe space and repair your ship with a repair laser in your space suit (press fire). It takes a bloody age and is obviously easier to dock at shipyard and pay for repairs but in the early stages its a viable option to make more cash on that knackered out pirate ship you just captured.
Salvage Insurance - A must for early on when you made your first few hundred thousand. Save anywhere in space per 3k. Having to dock each time gets a real ball ache.
Satellites - If your planning on trading at all a good idea is to drop a satellite in each sector. This basically tells the game you have a ship in sector and you can now see the stock/price of everything in that sector as if you were in it. Advanced Sats simply give you a bigger range to see on the map.
Deploying Satellites - Obviously you need to buy or build them first but there is 2 ways to deploy satellites. One is to fly to a sector and do it yourself via opening your freight bay (Shift+F) and selecting the satellites then dropping 1 into space. The other more player friendly method is to have a ship do it for you say an Argon Discoverer. To do this send the ship to a Teladi Equipement Dock and buy Explorer Software. Once equiped buy the satellites with the same ship and you will have a new option in Navigate Menu called Deploy Satellites. Select a sector and an area (middle of map) and off he will go covering the X-Verse
Exploring Zones - Sometimes it can be tedious to fly around a huge zone trying to find them gates, however your troubles are solved! Send a fast ship, say Argon Discoverer to buy explorer software from a Teladi Equipment Dock. Then you will have a new option in Navigate Menu for this ship, order him to fly to that huge dust cloud filled zone and explore. It asks for parameters so enter 99999 and he will cover the entire zone area. It may also be a good idea to equip him with a Triplex Scanner.
Border and Core Sectors - Each Nation has it's core sectors where shipyards etc reside. You can not enter these if the race doesn't like you very much else they will attack you. Simply raise your rep by shooting some pirates, trading or doing missions for their border sectors.
Xenon Sector - Don't **** with them or you'll die. These places will generally have capital ships along with a 46" LCD screen load of fighters. This is for later on unless your feeling frisky.
Obvious basics really, buy cheap sell high. Items will always be at their cheapest if the stock bar is full and will always buy for the most if stock bar is low. You obviously cant buy Energy from one solar plant and sell to another as they are producing it so run the energy to a weapons plant or something that consumes a lot of it.
Starting as Terran a simple single sector route is in scale plate green. Story will guide you here early on and theres simple Flower Farm -> Sun Oil sales route. However this zone is adjacent to a Xenon sector and can get dangerous.
Sector Trader and Universal Trader - You get this option when you buy a Trade command Software III (500k). Sector trade does as it says, select it and click a sector and it will do it's best to buy low and sell high everything in that sector. The pilot will gain experience per trade varying on money earnt and eventually at lvl 6 you can tell him to become a universal trader. These guys fly all over your explored zones buying and selling just like before but with a larger scope. Eventually these guys will earn you a fortune, but they need clear space to work and are pretty dumb if attacked. If you find yourself losing them in an area then you need to setup a patrol of some kind to defend the territory.
Factories - Simple rule really, only build if needed. For example if an area is always low on energy, build a solar plant. However that plant will need crystals to produce energy and that crystal plant requires food etc etc. You need to do your homework when buying stations. However a simple start would be a Silicon Plant which only requires energy.
Asteroids - You can't miss them really, huge balls of rock. Silicon, Ore, Ice (new) and Nvidium. You can build mines on these or mobile mine them. They can be blown apart and scooped up and can be towed to a station your building in the sector. If they get destroyed GOD will eventually replace them.
Tractor Beam - You can purchase a Tractor Beam at some Equipment Docks. This is a mounted weapon (rear) which requires a fairly big ship like an M6 so not something you'll do early on. With it you can tow asteroids into place out of a cluster for easy access or drag a station you built in the wrong place.
How to Buy Stations - You will need a TL class ship to do this, they are very cheap to hire and easy to spot since they're huge. If unsure fly upto one, press i and see if the class is TL. There's usually one in or around the sector of a shipyard. Simply Comm him and ask to transport something, he will state a fee per zone and then Comm again and ask to dock at shipyard. Once docked you can then purchase the station and tell him to fly to sector you wish it built. Alternatively you can buy your own TL which range from 9-40mil. Originally many people used the Split Elephant TL as a mini carrier as it was well shielded, had a few fighters and good weapons.
Stations - You need a fairly high faction to start building Stations not to mention a big bank account. For Example a simple single station would be a Silicon Mine. This will require power constantly and you might want to also sell the Silicon produced and for this you'll need a TS of some form like a Mercury to be assigned its Home Station to it. Once this is done you need commodity logistics software and tell it to commercially represent the station (In Trade Menu). However it's best off to start with to jump start it's economy by buying up any initial Primary resources required, usually Energy.
Illegal Wares - If you've played previous games this may come to a shock to you as Illegal Wares are now very much taboo. You can no longer build Space Weed Productions in the likes of Elena's Fortune as the Argon Fleet will not stand for it. Soon enough you'll be faced with a Defence fleet attacking your station. You will now have to build and protect your illegal stations in the Pirate Sectors. If you or your transports are caught carrying illegal wares by a scan the security forces will shoot you or your freighter down.
Complex Maths - You may have noticed stations come in M, L and XL if this has changed ignore me since I'm at work ;P Simple math calculation M = 2, L = 5, XL = 10. So when building complexes you need to take these sums into account, there was a previous very good Complex Calculator out and I will try find a new one for TC. But basics are if your building a Space Fuel M you will need a wheat farm M or L. If you use an L then you can obviously add another Space Fuel M and still have enough wheat.
Complex Building - Now we are talking big money, these cost a lot as you can be connecting 2+ stations together. For a full closed loop Solar Power Plant XL you're looking at a cost of around 100 million. However it will then supply power to whatever you want (within reason). To build a complex simply place 2 stations near each other and use a complex construction kit here which is also bought from a shipyard. If its the creation of a complex it will then ask where to place the terminal (where ships fly to dock). Make sure this is nice and clear so ships don't crash into your station giving you reputation lose! To add more simply join another station with the complex construction kit. The hard part and probably the most anoying in the entire game is lining it up right so its neat else you end up with spaghetti complexes.
Complex Calculator - This is a life saver when making large complexes to work out exactly what's required. - http://forum.egosoft.com/viewtopic.php?t=197763
30/12/08 - Added Complex Calculator
29/10/08 - Nearest Target, Active Guidance
24/10/08 - Illegal Wares
23/10/08 - How To Change Ship, How To Transfer Freight, Boarding Crews
22/10/08 - Deploying Satellites, Autopilot Docking, Exploring Zones, GOD, Tractor Beam, Buying Stations, Station, Complex Maths, Complex Building, Ship Controls Default and Classic, k key.