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after uninstalling the app, go to .wine/.....Program files and delete the dir containg the app to completely remove the app. also look in /opt, some distros put links for the app in there i think. If you mean removing from the menus, that depends on ur desktop. Just edit the menu and remove the app starter
If you mean the uninstaller menu, like when you remove a program in Windows and the name is still in Add/Remove programs, the only way I've found is to open the registry files (user.dat and system.dat) in a text editor and remove any entry lines that reference the particular program. This is the same as editing the Windows registry so be careful.
It's a good idea to take backups of the files before editing them -- like you'd backup a registry in windows. I myself usually just run the application's own Uninstall exe file, and this far it has worked all right. Wine has one good side - if you screw it up, just copy your wine's config file, remove it and reinstall, then either reconfigure it or replace the main config file(s). A lot easier than reinstalling Windows
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