I know this isn't limited to just LIszt's music, but he's the only one that can come to my mind about this subject right now.

I see in some of his compositions that when there's a trill with some one hand playing, let's say a C, and the other hand playing under it a B, the individual fingering for both hands is 3 2 1 3 2 1. Why's that?

A good example is on measure 84 of Hungarian Rahpsody #2 (I know I know... I'm as tired as you guys are of talking about that piece, but still).

Well, in general you should change you fingering each time you hit the same note twice in a row. It's a good practice to have and can help reduce tension in the wrist and increase the speed in the repitions. Trilling seems to be a slightly different manner because, obviously, you split the speed between both hands, but nevertheless if you can time the finger switching well enough and master it under relaxed conditions, the smoothness of the trill will improve.

I can't explain it much better than that but certainly someone else can...

It might not seem like such an essential thing for the time being, but finger switching (what's the proper name for the technique...?) is most definitely important in the long run, in pieces which might require long rows of single repeated notes in one hand, and at a fast pace.

Alborada...
mwahahaha...