I've been using WASD as much as possible ever since I first got used to it in some game or other way back when.
I've gone out of my way to get it working with older games as well:
People used WASD+mouselook in Quake when it was new, but it was a novelty because it wasn't the default behavior.
For Descent, I use the keyboard for 6-axis sliding plus roll (W/S = move forward/back, A/D = strafe left/right, Q/E = roll left/right, R/F = slide up/down) and the mouse for pitch & yaw. I tried playing with a flightstick and it just isn't accurate enough compared to a mouse.
For Doom, I use source ports that allow full mouselook. I've heard there are ways to turn off the vertical axis in the original engine so that you can use the mouse for turning, but I've never really tried it.
System Shock 1 is the only one I've really had a hard time using WASD on, but mostly because the mouselook hack has quirks (if you keep turning too far in one direction, you'll eventually hit some limit).
Daggerfall and Future Shock / Skynet were pretty much intended to be played with WASD+mouselook, but with concessions provided for people who hadn't yet made the leap from arrow keys.
I never bothered with ESDF over WASD, because it really just makes it possible to use Q & Z with my pinky instead of my ring finger. I don't find that very ergonomic, and it makes it harder for me to reach the tilde/tab/capslock/lshift/lctrl keys while making it easier to accidentally hit the Windows key.