As always, it depends on who you ask. My personal favorite is Echoes from the Album Meddle (which, by the way, is also my favorite Pink Floyd album). A Pillow of Winds runs a close second. Many people may not realize that Meddle is where the distinctive Pink Floyd sound that we hear on sbsequent albums started with Meddle as David Gilmour himself has said.
In my own opinion I think the best song by Pink Floyd is Learning to Fly. I think the best album ever made was Pink Floyd, The Wall. Even the movie made of The Wall is amazing. You can watch Learning to Fly here, along with several other Pink Floyd greatest hits. http://listverse.com/2010/03/13/another-top-10-pink-floyd-songs/
Fearless is probably my favorite. I guess I'm kinda a sucker for simple, expressive, pretty guitar hooks..and I've long thought of it as a perfect, solid song. It's definitely standing the test of (my life)time. http://www.youtube.com/watch?v=uCgQuj8v2gg