Try making a Filefilter

WinMerge handles this just fine. You want to create and use a Filter. Under Tools | Filters... | Filefilters, create a new filter or modify an existing one.

It will look like this:

## Ignore Java class and jar files
f: \.class$
f: \.jar$

## Ignore subversion housekeeping directories
d: \\.svn$
d: \\._svn$

Save it, then when selecting items to merge, select the filter you defined from the Select Files or Folders dialog box. Bonus points: It will save this and use it as a default for future merges.