I think the general trend is to use the equivalent warhammer sized bases. Thus:
20mm: humans, elves, skaven, dwarves, goblins, skinks, etc.
25mm: orcs, saurus, possessed, etc.
40mm: ogres, minotaurs, trolls, rat ogres, etc.
This keeps the models usable for your WHFB games if cross-compatibility is desired.
Unfortunately there are no official rules for Mordheim bases. I had thought that square bases were the official standard used in sanctioned Mordheim tournaments, but I learned that this was not even the case in this thread
about bases. The main thing is to make sure you use the same type of bases as your opponents. If one player uses a different size or shape than his opponents, it could be problematic.