I am just wondering if there is a list of all the meshes that have been found to have bad or missing collisions, and what has been fixed so far. As I would like to start going through and fixing some of them, especially as I am working on quests I find myself finding these meshes while testing.
If there is no list, I could start compiling a list together as I am testing.

I don't know of such a list... Check with Eloth when he's back from christmas but I'd say keep track of the ones you encounter. I usually ping him directly when I see some while testing my quests.
essentially all of them :p we used chunk merge but its glitchy. Ormin wrote a program to fix it, and we need someone to use it and batch fix as many envionrment meshes as they can.
Rocks are the main offenders
If someone can point me in the direction of this program, I don't mind doing it while I am working on quests, when I notice an out of place collision. As I was originally going to fix the collisions manually.
Ormin intended to write a batch fixer for meshes in future, but not sure when he will do it.
Two off the top of my head.
com_stone3way.nif
com_stoneendcap.nif
Those two are the reasons why people get trapped in that evil room in the Census office.
Fixed collisions on the following meshes:
- com_stone3way.nif
- com_stoneendcap.nif
- com_stoneendcap4.nif
This should allow players to move around that area in the Census office without getting stuck. I simplified the collision a lot as I figured that all these interiors will be remade at a later point and didn't want to waste a lot of time on a temporary fix.
You can get the fixed meshes here:
https://drive.google.com/folderview?id=0BzqpBc4MrAMXMEQtMFhB...
downloaded. thanks.
I have fixed the collisions on all stairs in Balmora (Exterior only at the moment) that were previously unwalkable.
Get the modified meshes here:
https://drive.google.com/file/d/0BzqpBc4MrAMXTDNtUUV3SHdTcEU...
Balmora Interior stairs now done. Unfortunately there is still a bit of a lip at the top of the stairs that will cause the player to stop a little. Dont think that can be fixed due to the steepness.
Get them here:
https://drive.google.com/file/d/0BzqpBc4MrAMXdUFCQVZmQms4TW8...
I downloaded and tested. This is perfect :) This will be in the next release along with the earlier links.
Seyda Neen lighthouse Interior/Exterior stairs fixed. See below post for link.
Little bumpy, but works perfect. No getting stuck at all, keep up the good work!
downloaded - thanks
All Seyda Neen stairs should be fixed now. This package also includes the Lighthouse interior/exterior.
https://drive.google.com/file/d/0BzqpBc4MrAMXekt6YzdoZnBqeXc...
Is there any way you can replace or fix the models for stairs generally used in caves? Whenever I debug caves, I always get stuck and have to jump up the stairs instead of walking.
Yeah I am working my way through all stairs, so eventually caves/dungeons will get fixed. Though bare in mind this is just a temporary fix. Eventually they will be replaced with new meshes, so I don't want to spend a large amount of time on a temporary fix.
This should fix some of the unwalkable ramps in Vivec and where ever else it is used.
https://drive.google.com/file/d/0BzqpBc4MrAMXZ0x1YkNYWW15T2s...
I will include those. thanks.