Might as well address some issues first...
Avatar is not anime. It's inspired by anime, and 500 % better than all the trash on those channels put together, but it's not made in japan.
Naruto is 220 episodes first part and almost 180 for the second part so far, which does NOT add up to 600 plus episodes. One Piece is creeping up towards 500 which gives it the potential to be a 1000 episode series. And yes, there are longer anime series than this...
The sea of Mediocrity is not up to 95% of all anime. Maybe 30 % on a bad day, but there are always series that just plain rock. As a science fiction fan, you should check out Legend of the Galactic Heroes. You'll only find it in fansubs, and it truly kicks sci-fi ass. 110 episodes for the main series, with 2 movies and four side stories, with the last one being 20 episodes. You really get to know and love the characters from both sides of the battle.
Let's put in Hunter x Hunter as another awesome series that deserves to be continued. In addition to only having one filler portion (which is actually good and 3 episodes long, and fits into the plot) it is completely amazing. One of my all time favorites.
Hellsing ultimate really puts the finishing touches on the hellsing series and gives us something that we can definately call 'adult' anime.
Black Lagoon is another 'adult' anime that I watch with great pleasure. Seriously, I'm so stoked that there is a third season, and it's about Roberta the maid. KICK ASS!
Most people have already hit on the fun series already. Suprisingly, I haven't seen any Nadesico, which is one of the best mecha-comedies out there along with Parallel Duel.
Any D&D fan that misses out on Slayers or Record of Lodoss war deserves to suffer. Oh, there are other great fantasy setting anime, but I'm just gonna mention these classics.
Haibane Renmei is about grey-winged angels who are born in cocoons as reincarnated souls. It's an odd little anime where everyone is confused as to why they are there and just who are the people that make it so the Haibane can't live as citizens.