How to exclude a Javascript file from Javascript Validation in Eclipse

well, probably I've managed to do what you need ;) It is a bit tricky. So my steps:

1. downloaded Eclipse PDT (to be sure that it works for you, because I use Eclipse for Java EE)
2. created project TestJS (it was JavaScript project)
3. created two files, test.js and htmlparser.js (last one copied from John Resig's site)
4. typed "broken" script in both of them, so Eclipse told me that there were errors in both of them
5. went to Project Properties > JavaScript > Include Path > Source, there is "Excluded" to highlight and press "Edit" button, here you are able to add what you want to exclude (file, folder, pattern).
6. I excluded "test.js" file, pressed apply...
7. ...and got a happy ending: now Eclipse point me out that there is error in htmlparser.js, but not in test.js ;)

ScreenShot:

Really hope that it helps!

Following from Maxym's excellent answer: since I usually keep all my JavaScript libraries in one place and the Eclipse validator tends to find unusual errors (perhaps entirely false positives), I used the Add Multiple option and selected the folders that contained those libraries. No need to update each time you add a file!