I recently bought a Kindle 4 and this device is simply wonderful. Reading an e-book is delightful and I recharged it only twice since I have it. One problem is reading two columns papers. It is just unreadable because too small on the kindle screen.
A solution consists in using K2pdfopt tool to convert such files into readable one column file. This tool (that you can retrieve from K2pdfopt website) can divide columns and even process figures that take several columns. Most of the time, it works very well.
You can use K2pdfopt as a command line tool. For example:
$ ./k2pdfopt -ui- -j 0 <paper>.pdf
Take a look at this page for other command line options.