I'm going to be buying a new crankset and bottom bracket (probably and ISIS setup or Octalink, haven't decided). My BB shell is 68mm and the BB spline is 113mm. I realize I need the same size with respect to the shell, but does the spline have to be 113mm? Will it not being 113mm throw off my chain line? Or does it all depend on the crankset/bb combination? Will one crankset give a different chainline from another, setup on the same bb?

113 is the common size for 68mm and 73mm shell BBs. With ISIS, at least, that spindle will give you proper chainline with most ISIS cranks. You start to encounter longer spindles with DH bottom brackets (to clear chain guides, etc.). Some BBs are 68/73, meaning you can use them in both 68 and 73 mm shells - -the non-drive-side cup 'floats' to cover either size (spindles remain the same size). Race Face makes some of these. FSA tends to be one-sized. If you think you might be moving parts to another frame sometime, look for a 68/73.

Awesome, thanks a lot dminor. This is along the line of what I was expecting, but I wasn't sure if there was some sort of unwritten standard among manufacturers or if it was a free for all go to hell sort of thing.

I think the unwritten rule is that the first one you buy will be the wrong size.