I don't think engines should be compaired entirely on eye candy to performance ratio.  Glquake may be scale very well and be very efficiently programmed, but it's a lot easier to program an efficient 3d engine when all you're doing is basic 3d geometry like in Quake 1.  And 1000fps on todays hardware is really a useless amount of perfomance.
The Source engine is definitely very efficient, but it's a generation behind as far as technology goes.  They don't use a lot of shaders, and the lighting and shadows are not up to the level of more modern engines.  Still, I think it fulfills an important role in todays games market.  There's no doubt it provides the best visuals for less than high end hardware (and lets face it, that's the majority of the market) and it gives a lot of freedom to the artists since they don't have to worry as much about performance, and that's why Source engine games end up looking so good.
The Doom 3 engine revolutionized lighting and shadows, so I gotta give it credit for that, but it has yet to prove it can make a game that doesn't look like doom 3.  Hopefully Enemy territory: Quake Wars will change that.  It doesn't run well on low end hardward, but the complex lighting/shadowing calculations it's doing gives it a good excuse, and I still think it is efficiently programmed.  If Quake Wars turns out good, Doom 3 could very well get my vote for best engine.
Oblivion looks very good, but I don't think that Gamebryo is a very good engine.  I think Far Cry did wide outdoor areas better and ran smoother as well.  In oblivion it's painfully obvious when the level of detail changes as you get closer to something.  Trees pop in, grass magicaly sprouts up in front of you as you move forward, and the geometry of hills suddenly changes as you get closer.  When you have such large view distances, you pretty much have to do level of detail changes, but Far Cry did a much better job of hiding this.  Oblivion is very cpu limited and in this day and age, most of the graphics work should be done on the graphics card.  The character models look fantastic, but the engine performs poorly for the visuals it's providing.
I haven't played any Unreal engine games recently, but from what I've seen it's in a similar boat as Source.  It's very efficient and runs great on older hardware, but is not visually up to par with with some of the newer engines, though possibly a bit more advanced than source.  Most of the major games that use unreal version 2.5 (the newest version) are multiplayer (UT 2004, Red Orchestra, Americas Army, Tribes Vengence) so they're more focused on performance than visuals.  Splinter Cell: Chaos Theory is the exception, but it being made for ps2 as well probably held it back a bit.  I guess the newest Unreal engine just lacks a killer app to show it off.
Fear is the only engine that can come close to matching Doom 3 when it comes to lighting/shadows, but that engine is an enefficient mess.  So for the best engine, I'll call it a three way tie between Doom 3, Source, and Unreal, with honourable mentions going to Far Cry.