With the upgrade to XCode 4.3, one of the significant changes is that the /Developer folder is gone and instead bundled within the /Applications/XCode.app/ content bundle. One thing that you have to remember is that for the command-line tools (of which now you should be downloading individually within the Apple Developer Site) is that you have to switch those command lines to use your new path, rather than the old Developer path.
$ agvtool Error: No developer directory found at /Developer. Run /usr/bin/xcode-select to update the developer directory path.
The xcode-select utility allows you to switch between versions of Xcode which makes it easy to correct the problem:
$ sudo /usr/bin/xcode-select -switch /Applications/Xcode.app
If you are wondering where all of the files that were previously under /Developer have gone you can find them by right-clicking on the Xcode.app file in the Applications folder and showing the package contents. The old /Developer/usr/bin directory is now in /Applications/Xcode.app/Contents/Developer/usr/bin.