The GOG version of UT99 worked fine in my 98SE test setup (Pent 3, GeForce 2MX, Voodoo 2, Vortex 2), but I ran the installer and applied several patches (eg. UT Bonus Pack 4, deleting the nGlide Glide DLLs, updated OpenGL renderer) on a XP setup and then copied the files over directly. I don't know if the GOG installer will work fine on 98SE directly.
I have the Steam version of Q3A, myself, but considering I've gotten it to work on that unit by overwriting the provided Q3A executable with the non-Steam 1.32c one, I believe the GOG version should work fine. ioquake3 hasn't worked for me, however, but I think it's a matter of recompiling with some needed libraries and/or using KernelEx.
Bear in mind that I only checked the single-player parts of the game, however, and cannot verify their usability on public servers.
CM-64, FB-01, SC-55ST, SC-8850, SD-20