I found this fantastic program to convert multicolumn pdf's into one column documents. That way any paper can be read and annotated in the edge.

Fairly easy to use. It is called Briss:
http://sourceforge.net/projects/briss/

Here is an example paper:
http://dl.dropbox.com/u/4794661/Para...0Resonance.pdf

and here is the result:
http://dl.dropbox.com/u/4794661/Para...ce_cropped.pdf