Applications/Xcode vs Developer/Applications/Xcode I have OSX 10.8 with Xcode 4.6.3 installed (it shows under App Store). When I Spotlight-search "xcode" I see two results: Xcode – Mac &amp; Xcode – Developer.

The first launches as expected, but with the second I get the following warning: "This installation of Xcode 4.2 requires Mac OS X 10.7 Lion. Install a version of the Xcode Tools that supports Mac OS X 10.8." and it quits instantly. Same if I try to launch via finder at Developer/Applications/Xcode.

I find this confusing - why does the app show twice and is there a way of removing the non-functioning version?

To further complicate matters, I have a folder Developer-3.2.4 containing this version of Xcode which also shows in Spotlight results - I followed a tutorial to keep an older version of Xcode when the buggy new version 4 was released. I assume I can safely delete that now?
You seem to have upgraded your system with older versions of Xcode present on it and missed uninstalling Xcode 4.2 while installing Xcode 4.3.

Xcode from version 4.3 onwards installs under /Applications. Only versions older than this (like your Xcode 4.2) install under /Developer. If you do not plan to boot OS X Lion from another disk/partition and use Xcode 4.2, you can safely uninstall it (do not just delete the folder from Finder).

To uninstall Xcode 4.2:


Open Terminal (Applications->Utilities->Terminal.app)
Type the command sudo /Developer/Library/uninstall-devtools --mode=all


To uninstall your Xcode 3.2.4 under /Developer-3.2.4:


Open Terminal (Applications->Utilities->Terminal.app)
Type the command sudo /Developer-3.2.4/Library/uninstall-devtools --mode=all


Reference:
How to remove Xcode from your Mac