Neither of these series had particularly strong endings. Haibane was really corny (granted, my opinion) and Mushi-shi didn't have a legitimate conclusion. I'm curious how these last episodes marked you?
I was really disappointed with the conclusion for Trigun when I first watched it, but it has grown on me.
Wolf's Rain. Its conclusion is pretty much guaranteed to make you go -- what? WHAT? WAIT WHAT!?!?!
Neon Genesis Evangelion. Neither good nor bad, but the introverted meta-narrative is memorable.
FLCL. Pure awesome. How to end fiction well 101.
I'm ambivalent about the conclusion to Monster. The final showdown, which lasts the final 10 or so episodes, is amazing and among the best anime produced between 2000 and 2010. The final episode in itself was a bit anticlimactic, though.
Noir and Haibane Renmei. Bad. Just bad.
.hack//sign. Great god's mercy, it's finally over.
An earlier poster mentioned Koi Kaze. I watched it so long ago that I don't remember what happens exactly, but I remember that it ended strong.