I have a 3D Panasonic plasma, and the glasses that come with it are specifically designed to accommodate people who already wear glasses:

As you can see, the lens is separated from the arm and a space is left to allow glasses-wearers to use them comfortably.  I've had a couple different people with glasses try them out and have no problem.  I don't know if other manufacturers are doing the same thing or not.

This is of course separate from the issue of the glasses that are worn in the theatre.  What I don't understand is how you could get glasses that are smudged from the get-go; every time that I've been to a 3D movie I get a new, poly-wrapped pair of glasses that has no evidence of previous use or uncleanliness.  I intentionally saw Toy Story 3 in 2D though, as I didn't find the 3D added anything to Up and the only movie I've yet seen where the 3D genuinely enhanced the experience was Avatar (out of 8 or so 3D movies I've seen).  I even ended up buying the Avatar game for 360 just because it's the only retail game that currently supports 3D (well, that and it was only twelve bucks).

ISR tried out GT5 in 3D. They noted that to gain the full effect of 3D you need to be close to the monitor  (or have a big HDTV). They came away impress stating they like it better than head tracking. 

Would you buy a special pair of 3D glasses that came with your eyeglass prescription? For around the same cost of a normal pair of prescription glasses?

If 3D catches on, I would.  People already buy normal glasses, transition lenses and sunglass prescriptions.. and contacts (I don't wear contacts, I cant stand putting stuff in my eye)