Jason, I get these all the time and it is very frustrating. I have no problem starting games and playing well into them, but I now have a folder I keep of CTDs. The reason I keep them in this folder is that I will occasionally go back and try them again. Sometimes they actually work, but mostly they are dead games.
Here are a couple of things I have tried with mixed success:
1. Dial down your games. I love playing with huge land maps and many civs, but that just slows down the game and causes many CTDs and MAFs, I think. Also, I have even sped up my games. I used to like Epic speed with an occasional Marathon game. Now I play Standard sized maps with the default number of civs at Normal speed. I still get CTDs though.
2. Save after every turn. If I get a crash, I go back 5-10 turns and play again. It is repetitive and boring, but sometimes it magically works and I am able to play on.
3. I hate to suggest this as I don't follow it myself, but try FFH2, FF or Orbis instead. I don't like them as much, but I find I am able to play further into these games with more extreme specs and finish most. Reason unknown.
I am a dope when it comes to programming and such and just take advantage of all the fine work the guys do for us in giving us these great mods. I just start a new game when I get the CTDs, file the old one, and hope THIS game will be better. Honestly, I really love the early game exploration and interaction with the animals most of all anyway - I am likely in the minority in this. If the game didn't bog down and crash all the time, I might feel differently.
One thing I have noticed a lot is the game is filled with all sorts of sounds, crashes, earthquake noises, you-name-it. It is probably unrelated, but I find there is usually one of these ominous sounds that precedes my crash.
I was thinking of upgrading my computer or getting one just for RiFE, but I'm not sure that would help much. I just keep hoping the new versions will cut out the CTDS, but so far...well, the early game is great. Did I mention that already?