Is it possible to take one of the older red/blue or red/green type encoded movies such as you might have on VHS or as a novelty and turn it into (black and white if necessary, or whatever) a more modern format whether outputting to shutter glasses or polarized glasses, in a format modern TV's could recognize?

The red/blue gives me such a horrible headache I cant even THINK about time i've spent trying to watch things that way without feeling nauseous... >_< But I really liked the 3d effect. And some older obscure movies that were done in a 3d version (like Starchaser Legend of Orin, one of if not the first computer animated movie I know of in the early 80's or so) are unlikely to ever see any Bluray or even DVD 3d rerelease... (i'm amazed it's even out in 2d frankly)

Yes, it can be done. There were a few threads with people discussing this. See here:
viewtopic.php?f=26&t=3488&p=25469

Here's a nice tutorial on doing just that. I've personally used VirtualDub to convert videos all the time and love it!
http://www.angelfire.com/film/puppetkite/VirtualDub3D/

It's not exactly point-n-click converting, but VirtualDub is extremely powerful.

I found that the sView media player can do a pretty good sudo de-anaglyph on the fly,

just set the input to anaglyph and the output to shutter, it's very watchable,

it even makes the lenses of your LCD specs look like they've changed colour!

http://www.sview.ru/en/