When it comes to graphics, yes, Doom 3 is miles away. No discussions there.
But I wouldn't be so fast to go hard on the art design of Doom 1&2, particularly the first one.
One detail I noticed was the clever use of circular shapes. Like it was said before, one of the problems with that game was the sprites awkwardly "turning" with you. But that isn't so noticeable with circles, since they don't have clear sides. So, what are the objects most frequently found? Barrels, barrels on fire, torches, lightposts, stakes... the dead trees and impaled guys look awkward, but even then (If i recall correctly) they tried to locate them in places either unreachable, or hard to circle.
The fixed camera helped to avoid many of those awkward angles too, unlike in, say, Duke Nukem 3D. But I think that was hardly their intention. A good but unintended side-effect, if you will
Then there's the color palette. Most walls in Episode 2 are green, with dead guys/blood to add some red. Same deal with some enemies for that matter, like the regular zombie (green/red) and cacodemon (red/blue), wich also had distinctive shapes to make them easier to tell apart. Maybe because of this is why I found all the more baffling the look of Quake, wich as far as I remember is a big brown mess (Though that was probablly because of technical limitations).
Now, I haven't played Doom 3, so I can't really voice an opinion on that one, other than acknowledge the previously mentioned advanteges/disadvanteges of 3D models. From what I heard and seen is dark as all hell, and as long as they used it to creat atmosphere, I'm okay with that. It sounds to me like a good way to hide the edges, too
While I agree the visuals in Doom 1&2 seriously show their age now, they're not a deal breaker to me, mostly because of those decisions. Still, I just felt like playing the Devil's advocate with the original Doom visuals for once, since most of the time all I hear around the web is it being a pixelated mess with cardoard pictures.
Just my 2 cents...