Of all the regeneration stories, I'd have to pick "Bad Wolf"/"The Parting of the Ways" as my favorite. It's been quite a few years since I've seen it but I still remember how excited I was when I first saw it. The game show stuff was funny. The Daleks were badass. The Doctor was even more badass. And they really had me going for a while when I thought they killed Rose. (And I liked Lynda. Shame she didn't survive.)
"The Caves of Androzani" was also a strong pick for me. With or without the regeneration, it's simply Robert Holmes firing on all cylinders. Sharaz Jek begins the tradition of bad guys shamelessly lusting after Peri.
"The War Games" would fill out my top 3. It's kinda long but mostly makes good use of its extended screen time. I love all the machinations between the War Chief, the War Lord, & the Security Chief. Lt. Carstairs & Lady Jennifer are great one-off companions. The initial mystery is quite good when you first think that you're just in the middle of a WWI historical story before you realize that something very different is going on. And the Doctor's farewell to Jamie & Zoe is heartbreaking. I like how Jamie thinks that they'll all just get away at the last minute like the always do, and how he seems a bit taken aback when the Doctor just shakes his head & firmly says, "Goodbye, Jamie." You really do feel that this is the end and that no one wants it to end this way. (I keep hoping that Jamie & Zoe come back on the new series at some point, if only to soften the blow.)
I've only seen "Planet of the Spiders" once but I thought it was fun. I especially like the 1 or 2 episodes where it's just the Doctor getting into a series of assorted vehicle chases. It's like Jon Pertwee has this laundry list of vehicles he wanted to have chase scenes with during his tenure and realized that it was now or never.
The regeneration itself in "Logopolis" is quite good but the rest of the story feels off. Tom Baker just seems to have already mentally checked out of the show. He never really had much chemistry with Tegan, Nyssa, or Adric for that matter. Plus, with Anthony Ainley as the Master and a general lack of humor to the whole thing, it feels more like a prelude to the Peter Davison years rather than a fitting finale for the Tom Baker years.
The 1996 movie is mostly terrible, although some of the stuff surrounding the regeneration is OK. The references to Frankenstein
& The Time Machine
feel a bit too on the nose. But considering it's trying to be obvious & over the top, it's quite successful in that respect.
I've never seen "The Tenth Planet." I'm waiting for the DVD.
I hated "The End of Time." I liked a lot of what they did with the Master but sometimes it seems like it's just a contest between Simm & Tennant to see who can go more over the top. And then Tennant's victory lap at the end takes too long, particularly since we'd already just revisted most of those companions 5 episodes earlier in "Journey's End." My favorite part of the entire episode is the last minute & a half when Matt Smith finally shows up.