1. Eccleston to Tennant in the Parting of the Ways. Although I felt Tennant's was more dramatic, I'm giving Eccleston's changeover the top spot for a few reasons. First, it was originally intended to be a total surprise to viewers, particularly those unfamiliar with the concept of the lead actor changing in this way. As such, it had the potential to equal the impact of the very first regeneration. Sadly, some buffoon in the BBC's PR department f---ed it up, but I don't feel I should penalize RTD or the series for that. Imagine having no idea this was coming -- and perhaps even expecting Rose Tyler to die which was what was at one point rumored.
2 (tie): Tennant to Smith in End of Time AND Hartnell to Troughton in Tenth Planet. I'm putting these two on equal footing. In terms of pure dramatics and emotional impact, nothing can compare to Tennant's extended regeneration (which as far as I'm concerned includes all the visitations - at its core, this was an extended version of the flashbacks we saw before Tom Baker and Peter Davison changed). And Smith gave it just the amount of manic energy (I assume he'll calm down in the regular series). I tied it with the first regeneration, which fortunately survives to some degree, and which deserves 2nd place for its historical importance, and also for its atmosphere. If you ever watch the reconstructed minutes leading up to the change, and then the change itself, it has a feel unlike that of any of the other (surviving) stories I've seen from the early years. And, of course, years before Bewitched confused American viewers by introducing a new Darrin, Doctor Who had already pioneered the concept, but did so in a way that ensured the show's survival to this day.
3. Tom Baker to Davison. I'd have loved to have seen Baker - still the record-holder for most consecutive seasons - get a walkabout like Tennant did, but the understated way in which he died and changed was dignified and worked well, even if the whole Watcher thing didn't make a lot of sense. (Ironically Baker's death was very similar to that of Bill Shatner's Jim Kirk in ST: Generations, which was condemned for being just as understated and low-key).
4. Davison to Colin Baker. Although the "Change my dear..." line turned things a bit pear shaped, the rather dramatic change, complete with hallucinations and a surprise appearance by the Master (believed to be dead at this point in the series) and Adric, plus the rather advanced (for its day) special effects, made this a near-perfect regeneration. Colin Baker's opening line "You were expecting someone else" was fantastic; they've have been better off ending the episode there.
5. McCoy to McGann. The first use of morphing to affect the change works well, and I like the parallels with the Frankenstein movies. I felt McGann overacted the "WHO...AM...I???" line at the end of the sequence, and I agree with McCoy's stated opinion that the regeneration should have been saved for a later series episode instead of confusing US audiences by having the Doctor change 20 minutes into the film. But on its own the regeneration worked well.
6. Pertwee to Tom Baker. I feel almost guilty putting this one down at #6 because Pertwee and Lis Sladen play it so well, and it was the first regeneration to truly sell the idea that the Doctor actually DIES when he changes, so for people who'd grown up with Pertwee over 5 years, this was likely a very impactful moment.
7. Troughton to Pertwee. This one didn't actually happen on screen, of course. All we got was a few moments of Troughton making funny faces into the camera and a cheap camera effect spinning him into the darkness. I watched War Games on DVD recently for the first time in about 15 years and it's more atmospheric a moment than I remembered, but still pretty lame compared to the first regeneration and those that followed. If I'd been in charge I might have done a "Wizard of Oz" moment with the sequence - have Troughton in B&W spin off into the darkness, and then cut to the color footage of Pertwee (or a body double if Pertwee hadn't been cast yet) falling out of the TARDIS. According to the DVD the ratings during the War Games nearly hit rock bottom; it's lucky the show survived, especially after such a weak regeneration.
8. Colin Baker to McCoy. I can't blame Colin for giving the BBC the bird after how they treated him. And good on whoever was in charge this day for coming up with the idea of McCoy playing both parts. But honestly, they could have come up with a better and more dignified way for the Sixth Doctor to die (especially given the foresight of the many terrific adventures featured later in the Big Finish audios).
9. McGann to Eccleston. Only because we never got to see the damn thing, not even McGann making some funny faces!
Alex