Definitely agree with /u/Symbi0tic, the ranking of "Best Anime" is completely dependent on what your tastes are. Bebop is a COMPLETELY different animal from most other animes, and the Bebop following loves it for that.

Personally, my biggest thing is the zeitgeist of the show. Humanity has fairly recently expanded its reach into the stars, and as a result, you get a frontiersman vibe from it. In comes the bluegrass/country sort of vibe, just a bunch of people trying to make a living in a hard, new world. that accounts for the "cowboy" portion of it.

The show also moves at fluctuating speeds, in terms of the events of a single episode. As bounty hunters, the crew has to be fast on their feet in situations, but sometimes are sort of just meandering about. Eventually, that song comes to an end, and they come to terms with the chip on their shoulder that they all came aboard with. That's the way they operate, the way they move. That's the "bebop" portion of it.

Another way it differs is that it's human. For one, one of the most obvious traits of anime in general is overly expressive characters. Bebop slows the speed down, and generally has more of a mature feeling to it. That's not to say it doesn't have poetic moments or cheesy lines, but just that it's more subtle in nature.

Another aspect to consider is the futuristic nature of the show. Most shows that are set in sci-fi have technologies that make them stand out and aren't questioned in the slightest. Cowboy Bebop, however, goes out of its way at times to make the setting feel dated. The destruction of the moon, nicks and scratches on damn near everything, hell, the Bebop itself is a repurposed fishing trawler. Tech doesn't work at times, Spike's constantly maintaining his ship, but that makes it feel settled in.

The combination of all of it is just so well put together, it stands resolute in my mind. Even 17 years later, I remember the first time I watched an episode. Just my 2 cents, though.