Freedoom 1/2, MM8BDM, Harmony, Chex Quest 3, that one new doom engine game starring the hedgehog, etc. are all gamepad compatible as the source port you use it on (and almost all of them have it fully). You can run about just every usermade Doom map using Freedoom if I remember correctly. I guess that all counts as freeware.
Also Xonotic.