I'm really sorry to say that I think Naruto was terrible. I'm rather surprised to see so many folks following it here. But then maybe you guys are like I was with Harry Potter at the end of the books "Well I've already dug myself a hole, may as well stick it out and see how it ends."
But that follows my general rule that any animated anything over 100 episodes has at least a 50% chance of not being worth the time.
I didn't like Eureka 7 at all either. As a mech guy, I just couldn't get over the "mechs on surfboards" goofiness.
Things I would second.
1. Akira (classic, and you'll like it if you liked GitS)
2. GitS SAC (fantastic music, old school cyberpunk style, better than the original movie)
3. Avatar (like Reboot, seems like a kids show that grows some teeth later)
4. Trigun (episodic with some greater arcs like Beebop)
5. Reboot (WHO IS NUMBER ONE?, sorry was just rewatching that the other day)
6. Beast Wars (Mainframe Entertainment made some good stuff, what can I say)
7. Starship Troopers: RC (better than the movie, closer to the book's view)
8. Death Note (Good if you like a show like Dexter or Columbo)
9. Evangelion. Series+Movies (The characters may have some problems but the logistics and the music are awesome.)
10. FMA: Brotherhood. (Worth watching the first twenty or so episodes of the first one too to get more detail on the parts they gloss over in the first 12 episodes of Brotherhood.)
11. WoH: Royal Space Force, beautiful animation and touching
Now lists of new stuff.
You like mechs at all (Transformers, Beast Wars, etc.?)
The UC Gundam stuff is great. Start with the 08th MS Team.
Patlabor is fantastic, series, OVA's everything. Patlabor the Movie is up there with some super pretty stuff.
Martian Successor Nadesico. Funny, interesting, and actually bothers with trying to make it's psuedoscience make more sense than Trek.
Super Robot stuff.
Gurren Lagann
Mazinger Z
GaoGaiGar
etc.
Space stuff.
The Magnetic Rose. Excellent space horror movie. Think Beebop mixed with Alien.
Planetes. This one needs no introduction.
Outlaw Star. If you like Beebop, if you like Trigun, you have to see this. Basically it was Firefly before there was Firefly.
Currently Airing shows worth checking out.
Thundercats 2011. Has a real Avatar vibe to it while keeping a lot of what made the old Thundercats cool as a kid.
Wakfu. An interesting take on a unique high fantasy.
Venture Brothers. How Johnny Quest would have realistically turned out when he grew up.
I can keep going but all the recommendations people have been making should keep you occupied for a bit I'm guessing.