Tenth Planet- pretty decent, introduces fun new enemies, but they and the Doctor are both absent for large chunks of it. Still, very striking and a strong contender.
The War Games - fun but overlong, and doesn't actually include a regeneration, cos it's off-screen.
Planet Of The Spiders- Mix of good and dire, woefully over-padded, but has some nice bits. Could have been a fantastic four-parter.
Logopolis- The first two episodes are turgid, and amazingly stupid (hell, "materialize the TARDIS underwater and open the doors") but the last two episode are great, and the regeneration really is fitting for the end of an era.
Caves Of Androzani- Easily the best regeneration story - full of doom and foreboding but without overdoing it. Great death scene for Five as well. As far as being a classic DW story overall, though, it's overrated. Great case and direction, but it is, after all, Power Of Kroll done dry.
The TVM - harmless fun, I guess, but didn't need a regeneration - there wasn't one between Troughton and Pertwee, after all - and bothering it robs us of some of the limited chance to get to know the new Doctor.
Parting of The Ways- not bad, though the regeneration feels tagged on at the last minute -for obvious reasons!
End Of Time- fun story overall, great Master story, but the actual regeneration tour itself is just stupidly overblown and has me shouting "get fucking on with it". If only he'd actually regenerated by surprise in The Stolen Earth... That would have been amazing!
So, I voted for Caves, with Tenth Planet a close second. If it was a vote for them as just "Best story" I'd have voted differently.