Ignore folders in solution compare with Beyond Compare

This is for version 3,

While you are comparing two folders you can go the menu Session->Session settings and go to the tab named Name Filters. There are several boxes to include or exclude files or folders; locate the one on the bottom right and on each line you can declare the folders that you want to exclude. There is an important combo box on the lower left corner where you can specify if you are going to use this settings for just this time or to use them everytime.

Another way to do this is simple look for the File Filters Toolbar (the one with a combo box and a pair of icons with a pair of glasses), in this combo box you can set your filter, for example -bin\;-obj\ and this will exclude the bin and obj folders.

I know this is old, but I came here looking for the same info for version 4.

Version 4 supports the same functionality but expose on the top toolbar in the session, just add the same -bin\;-obj\ in the "Filters:" text box: