I've been thinking about this one and I think there are a lot of good ones. I'll give you my top ten, let me know what you think.
10- Afternoon or Biding my time(live)
9- The Narrow Way(live)
8- Atom Heart Mother(live small band version)
7- Embryo(live)
6- Green is the Colour(live)
5- One of these days
4- Granchester Meadows or Daybreak(live)
3- Careful with that Axe(UmmaGumma)
2- Cymbaline(live)
1- Echoes

No, I'm not crazy. I purposely left off tunes from 'Darkside' and 'Wish'. It just did not seem fair.

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"And Doctor Strange Is Always Changing Sides"

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