If I had to pick one, I'd probably say Ghost in the Shell Stand-Alone Complex. Everything GitS is great, of course, but that first season of SAC is my fav of all the iterations.
Other Great Stuff:
- Blade Runner's the OG, and I think the sequel's just as good. The anime series for it, Black Lotus, is more pulpy than cerebral but I enjoyed it as well.
- I don't know if it counts, but I'll mention Patlabor here. If you haven't seen it, go watch it. Use this watch order
- Dredd 2012 is great, but again more pulpy. Haven't read the comics but I plan to get the "essential" TPBs
- Again, I don't know for sure it counts, but Cowboy Bebop is what I would call a masterpiece. I think everyone should watch it before they die.
- More subdued is A Scanner Darkly. I really enjoyed that movie as a teenager, but I haven't seen it in the last 15 or so years so not sure how it holds up.
- Biggest mindfuck would be Serial Experiments Lain. I couldn't wrap my head around it when I first saw it around 13, then I rewatched in my 20s and think I got the gist. If you like weird stuff that you have to think about to understand, it's great.