Duke Nukem 3D was probably one of the earlier FPS games that really encouraged modding because of Ken Silverman's Build Engine.
Even the enemy AI could be modified (albeit relatively limited) by editing the text CON files.
Anyone else remember playing over LAN with friends, dropping a Duke hologram in an elevator along with a bunch of pipe bombs hidden at its feet?
Back when I worked at the AG Group (famous for etherpeek) we'd play late at night we could hear each other screaming from our offices, and I'd walk out of my office terrified. The laser trips were the best. This game truly holds a special place in my heart.
We also had a really good LAN there.
It was a wonderful collection of rage inducing weapons: pipe bombs, laser trip mines, shrink ray (then step on them for the kill), freeze gun (any hit shatters for the kill), and the BFG.
We had LAN parties and would play for hours on end with custom maps we had built or downloaded.