Eclipse 4.2 on Mountain Lion: gatekeeper rejects as unidentified developer?
disable Gatekeeper ("Allow applications downloaded from: Anywhere")
run Eclipse once
reset Gatekeeper to a more strict level ("Mac Store and identified developers".)


Doing this has allowed me to start Davmail, also a Java app, after Mountain Lion initially claimed the binary was corrupt ("App is damaged and can’t be opened" error message) even when back on the stricter level.

Another option, as mentioned in John Siracusa's excellent review, is to do the following from the Terminal:

% xattr -d com.apple.quarantine /path/to/Eclipse.app


I have not (yet) personally tested this but John's a solid source.