Usually, if you don't put settings in registry, you use it mostly to get current Windows settings, change file associations, etc.
Now, if you need to detect if your software is already installed, you can make a minimal entry in registry, that's a location you can find back in any config. Or search a folder of given name in Application Data.
If I look at my Document and Settings folder, I see lot of softwares using the Unix dot notation for setting folders:
.p4qt
.sqlworkbench
.squirrel-sql
.SunDownloadManager
.xngr
.antexplorer
.assistant
.CodeBlocks
.dbvis
.gimp-2.4
.jdictionary
.jindent
.jogl_ext (etc.)
and in Application Data, various folders with editor names or software names. Looks like being the current trend, at least among portable applications...
WinMerge uses a slightly different approach, storing data in registry, but offering Import and Export of options in the config dialog.