This question will always spark debate, but there has already been one thread like this:
rabroad's Top 25 of Anime, 2004 edition
Also, here are two more lists from two American anime magazines:
Newtype USA's Top 25 of Anime, 2004 edition
Anime Insider's Top 50 of Anime, 2007 edition
I agree with rabroad and Anime Insider more, since they both list Cowboy Bebop as the greatest, but I also agree with Newtype USA, since it lists it as the second greatest, after Neon Genesis Evangelion. Overall, Anime Insider is the one I agree with most.
My personal top 10 list is:
1. Cowboy Bebop
2. Neon Genesis Evangelion
3. Samurai X: Trust & Betrayal
4. FLCL
5. Samurai Champloo
6. Gurren Lagann
7. Porco Rosso (and any other movie by Hayao Miyazaki)
8. Fullmetal Alchemist
9. Millennium Actress (and any other movie by Satoshi Kon)
10. Code Geass
Of course, it could always be argued that any anime considered the greatest could just be popular at the time, or that when it was declared the greatest, one greater had yet to come out. However, Cowboy Bebop has been considered one of, usually the nuraber one, greatest anime of all time for the past decade, so it's hard to argue that point in this case. But, more importantly, calling any anime the "greatest" will always result in someone arguing against it... *coughcowboybebopisthegreatestanimeofalltimecough* Ahem, excuse me, I seem to have a cold.