Anything with both Lis Sladen and Tom Baker on the commentary is bound to be pretty funny and cute, so that's most of the Fourth Doctor ones with Sarah in, I think... The Hand of Fear has a quite interesting documentary, as far as I recall. It's been ages since I've watched any special features so I'm having trouble remembering what there is...
As for the Seventh and Ace, I really like both Remembrance of the Daleks and The Curse of Fenric, good commentaries on them both and some interesting special features, plus they're both really good stories anyway.
If you like funny commentaries, anything with Janet Fielding is a laugh - Earthshock's a really sad story, but the commentary's hilarious! The one for The Visitation is great too. I don't remember why but I'm sure I actually cried with laughter at one point...
'Life is the most wonderful fairy tale of all!' - Hans Christian Andersen, from What The Whole Family Said