For my Master's thesis, I'm working on a real time visibility culling technique and I'm making a giant environment to test it.

The DooM 3 resources are very easy to get at since the .pak files are just a zip files. I was familiarized with the fair use policy today and am hoping that using a few of the textures and models should be allowed as long as it's for educational purposes and I'm citing them in some way.

Have you asked your thesis advisor? Why can't you make original stuff or have original stuff made?

You may or may not be protected by Fair Use, but unfortunately only a judge can actually make that determination if you are taken to court.

If you really want to proceed you should probably do as Tom suggests and ask your thesis advisor's opinion, but personally I would lean towards playing it safe and use something without the risk -- look for resources that are in the public domain or provided under a creative commons licence, or have someone create something new for you.

Hope that helps!

They said if I cite them it should be fine, and then I talked to the librarian and realized things are a bit more complicated than I thought.

And my thesis is the technical side, I don't really have time to make my own textures. I'm wasting too much time as it is making the models but that's only because it's fun for me heh...

I also realized I should be able to use high res fan made textures to replace the stock ones soon.

They said if I cite them it should be fine

Again, that can help but isn't necessarily true.

If you ended up in court and the ruling was against you the fact that you knowingly infringed upon iD's copyright (as shown by your citation) could result in higher damages being awarded than if you had naively done so. See also frob's response in another recent topic, citing similar rationale based on the concept of willful infringement.

As above, you may or may not be protected by Fair Use, but only a judge can decide that, and if it turns out you aren't protected it could actually be worse for you to have cited the source.

It's up to you whether or not you want to take the risk, but you should be able to find some freely available resources that don't carry the same risk; see OpenGameArt.org and Texture Warehouse for example -- you should be able to locate other similar resources with a little searching.