Do movies count? Well, I'll list them anyway, as Miyazaki stuff beats everything. Long running series tend to be pretty bad, as it's loaded with filler and poor animation, so I gave up on them.
Anime:
Spirited Away / Princess Mononoke
FLCL
Nausicaa
Kenshin OAV's
For "normal" anime series, I guess I'd pick stuff like Lucky Star, Haruhi.
For Manga, it's easily Berserk! Others like Kenshin, Monster, first half of Death Note, come close. The stuff I currently follow are also great. I tend to keep track of most of the popular stuff (Naruto/Bleach/etc), but my current favs are:
FMA, Claymore, Negima, Vagabond, Bakuman
edit: and Yotsuba&! To think I forgot my avatar...