Yeah, Judgement was Bakula's choice for the collection. In fact, in his interview for TATV, Bakula is very surprised to find out it got selected as a fan choice.
Honestly, I don't get the haterade toward the episode in question. Sure, Frakes and Sirtis put on a few more pounds, but I find the overall hatred of the episode quite amusing and cute.
Well, it is a pretty bad episode in general, but yeah, I agree the fan rage it generated was rather unnecessarily OTT, even by Trek fan standards. Granted at the time it aired I was developing an apathy to Enterprise and couldn't be bothered if they spent their finale on a ham-fisted TNG episode, but I still don't quite get the anger towards it. It's a bad episode, quite possibly one of the most disappointing in all Trek, but it doesn't deserve all the scorn it gets, even to the extent that Pocket Books even refuses to accept it as their canon.
Although, it was definitely a mistake to have it set on the Enterprise D as a side story to The Pegasus and try to fool the audience into thinking Frakes and Sirtis were eleven years younger. Why they couldn't have just set the episode post-Nemesis with Riker and Deanna on board the Titan I'll never understand.