I apologize for being a little late posting these but enjoy the next to last set in my countdown.
6. Shakugan no Shana II (Opening #1)
JOINT - Mami Kawada
I haven't personally seen the second season of Shakugan no Shana but I'm a huge fan of Mami Kawada. This opening sequence is epic! The song is well timed with the animation and I enjoy this song a lot. In fact it's one of my favorite songs to listen to.
5. Yu-Gi-Oh! Duel Monsters GX (Opening #4)
Precious Time, Glory Days - Psychic Lover
This is my absolute favorite opening from Yu-Gi-Oh GX. I enjoyed the 4th season a lot. Precious Time, Glory Days is an absolute epic song. The animation is epic and I enjoy this opening sequence a lot. Every character gets that appears in this season gets displayed and I love the part with E-Hero Neos bringing up the title's logo.
4. Black Rock Shooter
Bokura no Ashiato - Supercell
This has to be my favorite ending for an anime. The song is tranquil, the animation of the bird is peaceful, and I love this song. Bokura no Ashiato is a song that talks about life and the journies we experience everyday. I highly enjoyed the Black Rock Shooter anime and this song is really wonderful.