HERO: This game is the most flexible and internally consistent game I've ever played, earning it my #1 favorite ranking (Mutants & Masterminds is #2, D&D 3.5Ed is #3). I know that if I have characters of the same point level/disad limits, etc. will be balanced against each other, regardless of genre and setting...at least, insofar as PCs of a given point level can be balanced (rules gurus can abuse HERO just like any other system).
IOW, if I want to take a 300pt monster from Fantasy HERO and use it in Star HERO, I can probably use it unchanged.
In contrast, I have found that GURPS' various settings have enough variant rules and point costs for abilities that it kind of puts the lie to "Generic" and "Universal." For example, a PC based on TK powers in basic GURPS might be radically underpowered vs a PC based on TK powers in their superheroic setting at the same point cost.
(According to Jurgen Hubert- ENWorld's resident GURPSophile, the latest edition of GURPS does much to address this.)
GURPS: Better than any other game system out there, GURPS stats out all kinds of settings & useful supplements. I know I'm not alone when I say that even though I don't really play GURPS unless I'm being sociable (or playtesting), I will buy some of their supplements, like Martial Arts or their Weapon books. Whoever does their research does good work.
These are, of course, just my opinions.