I can think of a few offhand that I don't think should have been obsoleted.
First:
Terimakasih's Super Metroid 14% run, which was obsoleted by Cpadolf and hero of the day's 6% run. Admittedly, this has been beaten to death in the submission topic for Saturn's updated 14% run, so I'll keep it brief; the 14% beats the game legitimately, using a few glitches. The 6% glitches through almost the entire game via X-Ray Scope climbing out of bounds, and some RAM manipulation via dying to skip Mother Brain. The two really aren't comparable.
Second:
SprintGod's first Sonic 3 and Knuckles run, which was obsoleted by his second run. I think these two, again, aren't really comparable, for the reason that the second run uses the "scroll the screen and walk through stuff" trick, and the first one does not.
I also don't believe that Nitsuja's first S3&K run should have obsoleted SprintGod's second one, for a few reasons.
1. Nitsuja's run used both Sonic and Tails, which gives a lot more options than Sonic alone.
2. Nitsuja's run (both of them, plus the current one Upthorn hexed improvements into) extensively used the "zip through level structure" glitch, in addition to the "scroll the screen and walk through stuff" glitch; SprintGod's second run did not use zipping.
Third:
hero of the day's Chrono Trigger run, which was obsoleted by inichi's glitched any% run. This is the same basic situation as the one I outlined for Super Metroid; hero of the day's run beat the game legitimately; inichi's glitched past almost all of it.
The community has basically spoken on the Super Metroid 14% and Chrono Trigger runs, but I've heard nothing on the S3&K run, and so I wanted to propose that SprintGod's first S3&K run be removed from the obsoletion chain (essentially republishing it) and relabeled as a "low-glitch" run. Even when you compare it to the current S3&K movie, it still looks good. What do you think?
And what are some movies
you think should still be around?
(Shout-Out™: Thanks to alden for his Golden Oldies page, which is how I found out about SprintGod's first S3&K run.)