Hmm, this is a hard one. I grew up in the 90s (some can claim I'm still growing up, I am actually, considering I was 13 when "Y2K" "happened", so the 00's are also my decade). I dunno which songs are really "shaped" the 90s and 00s (especially since the 00s are still happening), so I'll just give some songs from those periods which I think can be considered really, really good.
Zombie (The Cranberries)
Hand In Hand (Dune - when I was young, I was a real fan of them)
Ice Queen (Within Temptation - Dutch gothic band)
Smells Like Teen Spirit (Nirvana)
Mmmbop (Hanson - I actually really hate this song, but I do know that the song was really addictive!)