I was out riding yesterday enjoying the beautiful 55* fall weather and long winding sweepers of SR 315 in Ohio when I pulled up to a red light on an incline. I know standard procedure is to hold on the rear brake to keep the bike from rolling back, but I wanted to see if I could slip the clutch to hold steady.  The bike stalled out, and I grabbed a handful of brake to keep from rolling into a semi that was behind me. Embarassed, but alright, I foot the rear brake and pull in the clutch and hit the starter button. The thing whirrs away merrily, but the engine doesn't wont turn over. I pull off to the side of the intersection and give it time to cool off thinking it was the problem (meanwhile being passed by about 15 or so bikers asking if I was alright  ). But after 40 minutes the starter still whirrs without turning over the engine. Finally, after I call the towing company and give it one last shot, it seems to slip, the engine backfires, and then it catches and starts.

TLDR:
Stalled on hill, starter whirrs engine doesn't turn.

Basically I'm wondering what could cause this problem, and if it is going to be recurring?

Starter whirring but not turning the motor = starter clutch is out.
Suddenly catching = starter clutch is well still bad but has 1-2 spots where it carches, maybe you ahve a spring or a pin bad, either way, the whole thign is ~30 .. .and swapping is a 1/2 hour job wiht the never to be found sliding hammer.
Ask for sliding hammer on the site someone has mine and there is a couple more guys that made em.
Stalling on a hill and trying to slip the clutch to hold it in place = stupid.
Cool.
Buddha.

By 'doesn't turn over' do you mean that the starter spinal and the engine doesnt, or do you mean that the engine and starter spin but the bike won't start?

Buddha's got the right idea, the starter spins freely, but none of the gears/starter clutch feel engaged. The engine doesnt 'move' (I don't know the correct term for pistons moving, but not firing up). I'll take it apart and see what I find.

Edit: Just went out to test it again, and it fires right up, no problem. What are the chances that it was just a fluke occurence? I kind of want to keep riding for the rest of the week before I start on getting ready for storage.

It may not fire up when oil gets nice and warm and everythign is much better coated. ... however not a reliable thing for long term, you can run this week if you're lucky and never have to start it hot, and put it away but you gonna have to fix it soon enough.
Cool.
Buddha.

Remember, if you ever need to just get home and the starter isn't working or your battery is low on juice, you can bump start it by coasting down the hill in 2nd or 3rd and popping the clutch once you get enough momentum. Can also be done by running along side the bike but don't drop it!