There are e.g. DarkPlaces, CrystalSpace, BlenderGameEngine, Torque, jMonkeyEngine, irrLicht, ShiVa, Linderdaum, ...
(lots to find here: http://devmaster.net/devdb/engines)
Those mostly also have some tools around them.
iodoom3 does bring some with it but those don't work on Linux (or Mac) because they are MFC based.
You don't get support by devs as they moved on to id tech 6.
So you're stuck with people like you that also try to get in.
And the first aid is missing.
It's not like UDK, Unity3D, BGE, ... where you start a new project and have the basics or just insert some things following an easy tutorial, press play and everything works.
No sample files. No base to build from.
Just pure source code.
Digging through iodoom3 for a university project is nice and I see a lot of potential.
But other engines are already free and open and are far ahead.
For gameDevs iodoom3 isn't currently an option.
Maybe if we get the source updated, new features included and the asset- and work-pipeline flowing…
(But why not use an engine that already has those features and tools and improve that…)
Also: motorsep from "Kot in Action" ("Steel Storm") is trying to get into iodoom3.