I think the knee thing is a bit up in the air. For my situation I thought riding it FG caused me terrible issues.
Now I am not so sure. It seems that all my bikes have some fit issues. Being that I ride several bikes each week it is difficult to track them down.
What I can tell you is if your knee is bugging you riding a FG is a terrible idea. That was the single most painful ride ever. 28 miles with my knee positively killing me. Being able to coast with knee issues is spiffy.

Anyhow, quite a few fit adjustments over the last couple months and I seem to be doing better. Now if I can fix my issues with my look keo cleats on my tarmac.....
Meh...

If I do alot of Fixed gear skidding or stopping without using the brakes, over a week or two I will have a nagging knee also. I'll Switch to my road bike for a day or two and its better.

What is the issue with your KEO's? I've been using them for three years now. I switched to the Grey cleats from the red ones and my knees felt better.

I commute every day on a mountain bike with giant knobs - this is definitely not the most "efficient" commuting choice, but I really like riding that particular bike. I'm in the process of building myself a commuter, but even then I bet I'll still ride my MTB half the time (mostly I just want the commuter because itll have slicks and looks like a beater - old old old huffy sanamark...I'm psyched to get this thing on the road)

One of my city riding buddies rides SS, and I love his bike. I don't see the big deal. Another of my friends rides a fixie, and that this is fun as hell. I think the real point is that we all have some form of non-car transportation and that should be enough. If efficiency is the standard we insist on measuring commuting by, I certainly don't fit the standard (I also often make beer stops and wild detours from my 'quickest route', I use odd gears sometimes, as mentioned I usually ride knobs, I refuse to commute with clipless/clips, my MTB has BMX platforms, blah blah blah).

The big picture: We all commute, at least sometimes, via a non-motorized form of transportation. I hope we all have fun while we ride - for me, that's the main reason I commute. We all experience a higher level of physical fitness, whether we ride unis, fixies, SS, road or hybrid or MTB or a damn wheelbarrow to work.

My right leg is splayed quite a bit. Trying to dial in my fit better and it has been difficult.
However, I was watching my right knee on a training ride yesterday and noticed it is moving quite a bit toward my top tube. I am now testing a specialized BG wedge to see if it helps. It is a fairly common issue and one would think I will figure it out eventually.