OPINIONS LOL to follow:
I never liked Trigun--I fail to see why it's considered anything above mediocre. Cowboy Bebop, on the other hand, was good. At the time I saw Bebop, my only exposure to anime was DBZ, Evangelion, and Gundam Wing. I felt that Bebop was better than all of these in terms of characterization, music, and plot, and for a few years, it was my favorite anime.
Since then, however, I have seen a lot more anime, of broader genres, and I no longer consider it the best. I think that while the majority of anime recently produced is pretty bad, the top shows of today are a little better than those of a decade or two ago.
Amongst fairly recent anime, Honey & Clover is probably my favorite, though I found a couple of episodes from Welcome to the NHK! to really resonate with me. The first episode of Macross Frontier looked really good; I would like it even more if some of the unnecessary fanservice was reduced, but that's not going to happen. Same with Gundam 00.