Ouch!

Don't get me wrong, I love my new toe clips and can't imagine how I used to get along without them.

Unfortunately, one of my feet tends to turn out. (I once had a very memorable horseback ride, when the eager-to-please critter I was riding, a little grey horse named Geist, thought I kept kicking my heel in...) Since the toe clip holds my foot in the proper position, this gets a little painful after a mile or so.

What do you think? Will the toe clip train my toes to point in the right direction? Or should I find some way to adjust it to accomodate my wayward foot? Any docs/physical therapists out there?

I take it you are talking about clipless pedals. You should be able to loosen the screws attaching the cleats to the bottom of you shoes, and adjust the angle of the cleats to the comfortable riding position of your feet. Dont continue riding with your feet in an uncomfortable position or you will do serious injury to your knees. Some pedals have more lattitude for foot rotation than others - mine are Shimano SPDs which dont have much so I had to fiddle gquite a lot before I got it right. I believe the Speedplays are very good for float.

I take it you are talking about toe clips. In which case, avoid tightening the straps too much. There is a fair bit of rotation available if you keep them loose. Also, avoid shoes with ridges which are designed to fit onto the pedal cage. These reduce the free rotation.
Forcing abnormal feet into normal positons is very bad for your knees.

If you are indeed taking of clipless pedlas, then both Time Attac and Speedlplay have lots of rotational float. You need free float, rather than one with a spring loaded centering system.
For your current system, investigate the different types of cleat available. Some systems have alternate cleats for different characteristics.

I am talking about toe clips. It doesn't seem to bother my knee at all (yet, anyway,) just makes my foot twinge. I'll try loosening the straps a bit and see if it helps--thanks!