First, I'd suggest perusing the 'net on articles about tectonics. This one in particular really helped me: http://csmres.jmu.edu/geollab/Fichte...on/Wilson.html
What that does is give you a general idea on how mountains form and why they tend to be where they are.
Once you've internalized that, I have some general guidelines that I follow: mountains tend to be either somewhat near a coast (Rockies, Andes), or where two landmasses have been "stitched together" (Himalayas, Alps).
Also, I've learned lately (and I mean VERY recently after 2+ years of mapping) that it's much easier for me to place mountains if I actually do it backward. I draw the rivers, then draw the mountain ranges as they fit between the rivers. Much much easier (at least for me).
Not a whole lot, but that's how I do it; hope it helps!