My pick is Shine On You Crazy Diamond, which happens not just to be my favourite song by Pink Floyd, but also my favourite by any classic rock band. I think it is the combination of knowing that it was written about Syd Barrett, the extremely emotionally powerfully music (e.g. Rick Wright's quietly devastating part IX, which to me symbolises Syd's loss to the band) and that fantastic moment when 'Syd's theme' comes in around 4 minutes on Parts I-V. It is also well paced, although the subject matter is very serious and rather tragic it's not 25 minutes+ of doom and gloom - the use of lap steel in Part VI is probably the most striking example of a sudden change in pace which keeps you listening.
Of the shorter songs, that's to say not including suites or extended pieces, I'd probably pick either Time (to me this brings together virtually everything that is great about DSOTM, with a fantastic Gilmour solo to boot) or Comfortably Numb (great and hugely effective combination of Waters' and Gilmour's vocals, powerful lyrics, especially in the chorus, and that legendary guitar solo).
Re:recgord27 - How I wish Pink Floyd were overplayed here! Be careful what you wish for of course, but sadly their music is probably better appreciated across the pond than it is in their home nation due to the lack of classic rock radio stations in the UK, at least where I come from - this means all of their albums are generally something to be discovered, rather than a band you constantly hear on the radio.
Grantchester Meadows is a decent shout, it has a very nice pastoral feel to it (and is quite pertinent to Roger Waters, for anyone who doesn't know Grantchester is a town in Cambridgeshire which is near where Waters grew up) - in a similar vein I'm rather partial to David Gilmour's underrated Fat Old Sun from AHM, as well as to the often (unfairly) derided Alan's Psychedelic Breakfast.