I've liked a lot of shows that got cancelled, but they had decent runs. I would agree with your Northern Exposure pick, even though I thought it was weakening considerably as it went along, and had pretty much run its course. It was still a great show though.
Enterprise is another. I'm glad to at least have gotten the 4 seasons.
As far as shows cancelled WAY too soon, I would say at the top of my list would be:
Freaks and Geeks - One of my all-time favorite shows. Every time I watch through the episodes it pains me to think of what could have been as far as further developing the characters. It's easy to recall this as a FOX show, since they notoriously cancel great shows, but NBC was actually the culprit on this one. Give FOX some credit though, as they did cancel Judd Apatow's almost as good follow-up series, Undeclared.
Greg the Bunny - What a great and fresh show this was. I loved the cast (including all the puppets). I'm thankful this was at least released on DVD so I can enjoy the few eps that we got before FOX axed it. MTV now has the spinoff Warren the Ape, so GtB fans at least have something out there to enjoy.
Andy Richter Controls the Universe - I always liked Andy on Conan, and thought he was hilarious in Cabin Boy, so I was thrilled he got his own sitcom. Just another in a long line of shows that were just too clever and fresh for FOX to stick with. Took this one a long time to come out on DVD, but thankfully it finally did.
The Tick - I thought this was a brilliant show, both in the comedy writing and the look with the sets and costumes. Great cast too. Thanks again for pulling the plug FOX. If all these FOX shows were so bad, why do they bother putting them out on DVD? Well, I'm glad they do, but I still think that network is run by a parade of morons.
Arrested Development - Pretty much anyone who appreciates great and truly clever sitcom writing has at least some level of appreciation for this show. Of all the shows that FOX has cancelled, this one shocks me the most. Amazing how many shows FOX has had that were either nominated for or actually won awards, that they turned around and cancelled. I'm amazed that they didn't cancel The Simpsons after the first season (and they stuck with Married...With Children??!!).
The Oblongs - One of only two shows on my list not cancelled by FOX. This one was on the WB. Obviously, this show was not mainstream enough for primetime TV. It's much more at home on Adult Swim. Too bad there weren't more episodes. Will Ferrell was great voicing the main character. In fact, the entire cast was quite good.
The Ben Stiller Show - Yet another FOX casualty. Was exceptional for a sketch comedy show, and I really liked the cast of Janeane Garofalo, Andy Dick, and Bob Odenkirk. I found a high percentage of the bits to be quite funny, unlike SNL.