1. Make TortoiseSVN ignore /bin and /gen directorys.
Right Click the directory, Tortoise->SVNSettings->General. Under "subverion", add "bin gen" to global ignore pattern.
2. Make Eclipse ignore .svn directories
Window -> Preferences…, Java -> Compiler -> Building. Under “Output folder” add “.svn/” to “Filtered Resources” (so that you get “.svn/”).
refer to http://blog.projectnibble.org/2009/08/11/repost-make-eclipse-ignore-svn-directories/
3. Make Araxis Merge ignore /bin and /gen directorys.
View->options->Folder Comparisons->Filters as the following figure.