I use the Eclipse 3.5 IDE with the Subclipse plugin to access my Subversion repository. Most of the time it works really well. However, this morning it kept asking me for my password for every comparison in the Team Synchronising perspective despite having my password stored in the encrypted store.
I searched around on the Subclipse wiki and found that the details were stored in the Windows %APPDATA%\Subversion\auth directory, which is C:\Documents and Settings\username\Application Data\Subversion\auth on this computer. As I was only having problems with one repository I did not want to delete all of the passwords. This meant opening up all of the files in the svn.simple directory and looking for the repository URLs. Fortunately, the files are all text but the file names are seemingly random hex digits.
After deleting the file for the problematic repository I just went to Eclipse again, entered my password once and the problem was solved. I did not even have to restart Eclipse.
Enhancement request 2775 on the Tigris issue tracker will hopefully be looked at in release 1.8 but it has been waiting for attention for almost 3 years now.