I like all of them. I've always believed that Roger Waters is one of the best song writers ever; he even ranks up there with those other two guys (what were their names, again? Lennon? McCartney? Something like that). I've always been partial to his "theme" albums, like "Dark Side Of The Moon", and "Wish You Were Here". I've even been a big fan of his solo projects, and am the only person I know who still has a copy (vinyl, of course) of "Music From The Body".
I know its a safe choice, but I think "The Wall" is their best. A great blend of Waters' writing, and Gilmour's singing --- not to mention some excellent guitar playing.
Second choice for me would probably be "Animals", or "Wish You Were Here".