hmm... Well my top three would be as follows:
3 -
Super Driver by Aya Hirano [The Melancholy of Haruhi Suzumiya]
I'm not a big fan of cheery music, the majority of it just isn't my taste of music, but I'm a big fan of Aya Hirano, just seems like the exception the rule, and I thought Super Driver was a good, sutable opening to Haruhi, a usually cheery show that suits the theme of having fun.
2 -
Kaidoku Funō by Jinn [Code Geass]
I'd only say this as Kaidoku Funō is one of my favourite songs, so having it as an opening to a show I love put it on this list.
1 -
Rise by Origa [Ghost in the Shell: Stand Alone Complex 2ndGIG]
Fantastic and rather inspirational lyrics, a very strong opening to an equally strong show.