AI War is a 32bit program for a lot of good reasons, and the one drawback of that is that it can only use 2GB at most of system memory. This is normally not a limiting factor at all, because most of the time the game uses about 500MB of memory at most, and even in extreme cases such as the 201,000 ships example that only uses about 1.1 to 1.2GB of memory normally. During game saves it will use about 400MB more. During certain high-frequency command issuances to a lot of ships in a huge game of this sort, that can also cause temporary memory spikes which can, in the worst case, cause this error.
Keith is going to add pooling to a couple of more internal objects that we use in order to hopefully minimize the load on the memory heap in situations such as the one you are describing, which should alleviate the issue. The game has to be in a really extreme state of resource usage before this can even become a problem, though; when moving around that many ships for the moment, issuing orders to fewer of them at a time is a good idea, likewise giving orders less frequently is a good idea. That is super hackish, obviously, but is a good workaround for the short term. With 12,000 ships on one planet, though, that game must be one heck of a beast; normally the upper end of expectations is more like 4000-7000 total for a human player, excepting multi-planet starts and similar.
It's also possible that some other program is using a global windows hook that is causing some memory address fragmentation; MSN messenger has been pointed out as a culprit for this in the past. If your memory usage is spiking unusually highly without a huge number of ships in the game, then that sort of thing is what it is (and that would affect other programs and system performance in general, if that's the case). From the little information I have so far, my bet is that your savegame is just absolutely monstrously huge (beyond what would be playable on most hardware, but with your supernice rig the memory instead becomes the limiting factor). Hopefully the next beta version, which will hit Monday, will provide some degree of help for that sort of extreme edge case; we always try to avoid having any such memory errors even in the really out there cases, of course.
Thanks for the report!