As a developer, tools that store configuration/options in the registry are the bane of my life. I can\'t easily track changes to those options, can\'t easily port them from
Registry reads and writes are threadsafe but files are not. So it depends on whether or not your program is single threaded.
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.
Is the world going to end if you store a few window positions and a list of most recently used items in the Windows registry? It's worked okay for me so far.
HKEY-CURRENT-USER is a great place to store trivial user data in small quantities. That's what it's for. It seems silly not to use for its intended purpose just because others have abused it.
If you are developing a new app and you care about portability you should NEVER store data in windows registry since other OS don't have a (windows) registry (duh note - this may be obvious but gets often overlooked).
If you're only developing for Win platforms ... try to avoid it as much as possible. Config files (possibly encrypted) are a way better solution. There's no gain in storing data into the registry - (isolated storage is a much better solution for example if you're using .NET).
In .NET there really is NOT ever a need.
Here are 2 examples that show how to use Project proerties to do the this.
These examples do this by Windows User Project Properties, but the same could/can be done by Application as well.
More here:
http://code.msdn.microsoft.com/TheNotifyIconExample
http://code.msdn.microsoft.com/SEHE
Settings that you want to have available in a user's roaming profile should probably go in the registry, unless you actually want to go to the effort of looking for the user's Application Data folder by hand. :-)