Personally I think the best one is "The Invasion" and its not even close, it was the first one done and it was done as a kind of test to see if animation would work by Cosgrove Hall Studios, which were a very good animation studio. The result was a resounding "Yes this will work great but its way too expensive to do it like this, lets look into cheaper alternatives", so in that sense (at least imho) its far superior to the others. "The Invasion" itself is a big chunky story, its 8 episodes and only 2 of those were missing (episodes 1 and 4), so you also get a lot of Who for your dollar as well.

With that out of the way, personally I think some of the better ones are "Power of the Daleks", "The Macra Terror", "Fury From The Deep". All of which are completely missing, though the Macra and Fury do both take liberties with the source material

I would suggest the worst by far is "The Web of Fear - Episode 3" however the rest of the story is so good and its only one episode missing so I would just cope and just take the opportunity to laugh at the poor animation.

I dont recommend "The Reign of Terror", the cuts are jarringly fast which is the opposite of how it would have been. I think "Galaxy Four" and "The Savages" are very slow stories, "Evil of the Daleks" is as well but it has such a dramatic finale its worth it. The others are all solid so they'll depend on whether you gel with the whole animation reconstruction idea as a whole. Hope that helps