Honestly, the desire to rule and control everything or to obtain an ultimate power, whilst a cliché, is probably one of the most realistic motivations considering human nature (it also applies to non-humans, obviously).

Likewise, the desire to destroy everything has become a clichéd villainous aim, although the motivation behind it can vary. The view that nothing truly matters and that life is imperfect is one such motivation; as one with an existentially nihilistic outlook myself, I can assure you that it is quite plausible.

I do like villains that have a different motivation to the two above, but it can often fail to work; Ultimecia is a good example of that.
As JC said, special mention should be given to GLaDOS for having a unique motivation for her actions and actually making it work.