With Xcode 4.3, Apple has moved the content of /Developer to the usual places for applications etc. Filemerge is accessible by starting Xcode and then accessing Xcode -> Open Developer Tool. If it's not listed there, select "More Developer Tools" to install it.
Physically it's part of Xcode.app (
Xcode.app/Contents/Applications/FileMerge.app) and can be executed stand-alone by inspecting the package content of Xcode.app. If you really need it outside of Xcode often, you can also create an alias/symlink to start it directly (or just drag it into the Dock).