Limited Resources

It's quickly obvious that growth will be restricted by the availability of certain resources, but not immediately apparent which are actually the most important ones to worry about (especially in the long term).  A player will immediately see that the ability to grow one's fleet is limited by the availability of minerals and of cash.  Clearly these are the key resources to worry about, right?

Wrong!

Don't get me wrong, they are important, but usually they will result in localized short-term bottlenecks, which while they are better avoided, will not usually be game-killing.

So what are the key limited resources?

This is based mostly on my own limited experience, and some reading, but it seems to me that each of the following is a resource, that will ultimately cause you far deeper strategic difficulties than supplying minerals and cash:

• Fuel.  An army marches on its stomach.  In several games I have found myself with some mighty marauding fleet bearing down on an enemy home area, only to discover that it doesn't have enough fuel to see through its mission.  The result is that it has to cool its heels while it waits for refueling to catch up.  Always plan your fuel logistics carefully.  Bring tankers (Q Tankers, Neutronic carriers, etc.) with you.  If you can get them, ships which manufacture fuel (Cobols etc.) are invaluable.  Expecting to be able to pick up fuel from the enemy worlds you conquer as you go is all very well in theory, but it seems to often fail in practice (either because the enemy hasn't developed their worlds, or because they have taken a scorched earth policy and denuded them before they can be taken).
• Colonists.  Unless you are playing the Cyborg (who can ignore this point I think), you basically have to carry all your colonists out from your homeworld.  This has two consequences:
  1. You have a significant logistic process to manage to ensure colonists continue to flow out as you conquer more territory.  In particular it's usually good to follow up a battle fleet with some camp-following colonists!
  2. Population growth on your homeworld is very important.  You need to maximize this, so don't tax them more than you can avoid!  I find 'pulse taxing' works well - most of the time have your homeworld at 0 tax to maximize population growth, and every now and again (ideally when happiness is back at 100, and not until you need the cash), tax them at whatever percentage will reduce their happiness to 70 for one turn, then go back to no taxation until happiness recovers.  This way you have maximal population growth about 5 turns out of every 6.
• Ship slots.  Unless you are playing a game with a standard ship limit (500), but only a small number of players (so only private games, set up that way), then you will very quickly hit the ship limit (in beginners games this seems to happen around turn 30, with more experienced players I believe it happens nearer turn 20 due to higher priority given to starbase production).  Even with the new priority build system, the total number of ships in the game will not exceed the ship limit by much (and over time it will tend to the ship limit, since PPs earned for ship destruction are always less than required for their creation).  That essentially means that every ship you own is one the other players don't.  Horde those slots.  Filling ship slots quickly (and/or generating PPs ahead of the ship limit) means having as many starbases as you can reasonably manage.  At first I did not realize how important it was to increase your starbase count (aside from the obviously useful ones on Ghlipsoidal and Human native worlds), but the more I have played, the more I have reached the conclusion that it's best to pretty much spam starbases everywhere you reasonably can - even if you cannot feed them all in mineral (or cash for tech levels) terms, they at least produce PPs for you, and significantly add to planetary defense.  Also most races have some useful low-tech ships they can build, even if not all races can leverage them as well as others (go, Fascists!)
• Natives.  I'm pushing the boundaries a bit to call this a 'limited resource', but they are at least sparse, so identifying and controlling the right ones is important. Early on you want to colonize native-populated worlds as top priority (if you can build something that bio-scans, doing it really early seems good to me - I have played the robots in quite a few games, and I now build a bio-scanner on turn 1 with them).  Once you identify useful native worlds try to exploit them efficiently, or at least the best of them.  This means getting sufficient colonists on them to maximize taxation in the case of high government types, and to maximize supply production in the case of bovinoids.
• Minerals and cash - ok, they are important too, but usually they will tend to be more localized shortages than global ones until quite late in the game, so really they are more of a logistic issue than anything else.  Later in the game, as everything starts to become mined out, it will be important to have alchemy ships generating new minerals (and possibly fuel unless you get your hands on some Cobols or similar).  As such it's generally a good idea to build a couple of Merlins before the ship limit hits (you don't want to be spending PP on them really) and getting them to appropriate worlds to operate at (ideally high pop Bovinoid worlds).

Oh yes.  One other easily under-estimated limited resource is your available play-time!  I really screwed up on this since everything seemed so fast at first, and find myself somewhat over-committed (trying to play 7 games at once).  The result is that I cannot give any game the time it deserves to think about and play each move.  Ramp up slowly to, find your comfort level.