There's a lot of nostalgia on this list so take that for what it is. This is my top 5 because I can't really put together solid concrete reasons why anything lower is in my top # anything.
Cowboy Bebop - Just the epitome of what anime is and can be as an art form. A ridiculously amazing blend of music, animation and writing that tells a rich and deep story that stays timeless even 20 years later.
Super Dimension Fortress Macross - the first anime I ever fell in love with, even if it was under the guise of Robotech at the time. The story and themes are timeless and never something I ever expected to see in a "cartoon" when I was a kid, the music (both versions) is great and the animation holds up relatively well for being from the 80s. The fact it has spawned such a sprawling and successful franchise over the years should speak to its greatness.
YuYu Hakusho - to date, my favorite Shonen. Awesome characters, great writing and action that never gets old. Like the others on my top 3 it gets massive bonus points for its English dub featuring such stand out titans as Chris Sabat, Justin Cook and Kirk Thorton that feel like they've been in basically everything at this point.
Fullmetal Alchemist Brotherhood - self explanatory, I saw this for the first time way after I was exposed to the hype around it and it still held up. Great story, characters, themes and action.
Dragonball series - I grew up on this shit. Android/Cell Saga is the best dont @ me. This series is/was so much better with the Bruce Falconer score, and it's hard for me to go back and rewatch any other version.