One of my favorite subjects. I'm more well versed in TV series than feature length, so that's where my recomendations lie, though they do take more of a time commitment to fully enjoy.
Chris, I think you specifically would enjoy Nadia: Secret of Blue Water. It's loosely based on 20,000 Leagues, and in turn Disney's Atlantis is loosely based on Nadia. Very entertaining adventure story.
A common theme in anime is the end of the Samurai age in Japan, as the government embraced the use of firearms and Samurai were being forced to give up their swords. My favorite series from that genre is Ruroni Kenshin. Beautifully animated, great characters. And it's fairly non-serial (there are some larger story elements that progress through the series as characters are introduced or written out but for the most part each episode is self contaiend), so it's easy to stop and start at your leisure.
The ever popular mech-suit genre is headlined by Macross. There's a lot of material in the Macross series, but Macross Plus is my favorite, an excellent movie.
That's the top of my head list.
Edit: Oh, and in terms of classics, Ghost in the Shell and Akira are two must-sees.
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