Using winmerge can be difficult if you could not filter the files you intended to compare within a given directory, specially if you are using a repository tool like SVN or CVS which creates a housekeeping folder for tracking. Below is a filter that can be used to ignore SVN and CVS folders.
## Ignore class and jar files
f: \\.class$
f: \\.jar$
## Ignore cvs folders
d: \\\\.CVS$
d: \\\\._CVS$
d: \\\\CVS$
## Ignore svn folders
d: \\\\.svn$
d: \\\\._svn$