yeah, H264 crashes my AE alot, too. sometimes it works, sometimes it crashes.
If I'm just posting something on the web, I render out of AE as a sorenson 3 MOV, then compress AGAIN with sorenson squeeze. If I render out a real short film, something I will want to make lots of different versions of, I render out a TGA sequence as a master, then render it out using that master frame set later in whatever formats I need.
My favorite preset in Sorenson Squeeze is the QT HD 480 (or something like that). But you should do a bunch of tests to compare file size with quality and see which one works best for you.