I also have problems with the post-Leland episodes. I wouldn't say the show turned completely "bad," per se; it's more like it turned into something that, if I hadn't already known that the show was capable of greatness, I wouldn't watch at all. Mike's right that the comedy really overtook the show for about 4-5 episodes, and the underlying sense of menace that had previously made the show so great was missing entirely. Which wouldn't be so bad if the comedy was good enough to make up for it, but I thought all the comedy stories - Little Nicky, Super Nadine, Ben Horne's Civil War obsession - were pretty much clunkers.
It felt like the only dramatic arcs the series was dealing with for a while were James' weird out-of-town affair and the Josie/Thomas Eckhardt stuff, and I had to struggle to care about either one. Jacques Renault was a pretty unremarkable villain. I know some think that the series started to pick up again once Windom Earle entered the scene, but I was never able to go for him, either. Too whimsical and cartoony to really feel like a menace. Really, those disguises? Terrible. (The Log Lady one was pretty good, though.)
Also - and I may lose a lot of people on this - I hate how the show expanded on the mythology behind the Black Lodge. Of course, the scenes that take place in the Black Lodge are the show's definite highlights; I just don't like how they explained exactly what it is, how it can be entered, what's inside it, etc. They completely sapped the thing of all its mystery. And honestly, most of the mythology surrounding the White/Black Lodge is really kind of dumb. It's standard heaven-and-hell/purgatory stuff, which just feels too pedestrian for a series as original as TWIN PEAKS was at it's best.
Generally, I feel that the further the show got from the ultra-realism of the first season, the worse it got. The first season, despite the Red Room sequence in Episode 2 (which was itself a dream sequence), is played completely straight. There were always hints of the unreal (Cooper's rock-throwing intuition display, the visions of Bob, etc.), but they never overpowered the physical world. It was when these concepts that were only hinted at in the first season became concrete in the second that the show started to go downhill, I think.
Really, I don't like that the Black Lodge is a real place that you could visit. I don't like how Bob is an actual spirit that can possess people. These things had much more power as abstractions. Lynch is a master at throwing in the kinds of things that, even though they're never explained fully, you get a kind of understanding of what they are and what they're supposed to mean. And when Lynch left the series, the writers fell over themselves trying to fill in the blanks and explain things that Lynch himself didn't even have an explanation for. And really, the series would've been better off if we never knew any of it.
But none of this takes away from just how incredible TWIN PEAKS was at its pinnacle. The first season is a near-flawless streak of greatness. (I have some problems with the "Laura's funeral" scene, but whatever.) All of the Lynch-directed episodes in Season 2 are terrific. In particular, I think the episode where the identity of Laura's killer is revealed is the series' undeniable high point. (Trying not to say 'peak' too much.) I was blown away by how amazing Ray Wise is in pretty much every scene he's in. Why the series killed him off, I'll never understand. That's another thing: I know ABC pressured Lynch and Frost to reveal Laura's killer, but I don't see why they actually had to CATCH the killer so soon afterwards. I think they could've gotten some more mileage out of that post-reveal shock.
This post is too long, so I'll quickly note that I also watched FIRE WALK WITH ME and thought it was absolutely terrific. Definitely one of Lynch's best, and better than all but the very greatest moments of the series.