I actually like MY JavaScript files to be validated, but I definitely don't want to validate and deal with trivial warnings with third party libraries.

That's why I think that turning off validation all together is too drastic. Fortunately with Eclipse Indigo ( 3.7 ) you can selectively remove some JavaScript sources from validation.

1. Right click your project
2. Select Properties -> JavaScript -> Include Path
3. Select Source tab. ( It looks identical to Java Build Path Source tab )
4. Expand JavaScript source folder
5. Highlight Excluded pattern
6. Click Edit button
7. Click Add button next to Exclusion patterns box.
8. You may either type Ant-style wildcard pattern, or click Browse button to mention the JavaScript source by name.

The information about JavaScript source inclusion/exclusion is saved into .settings/.jsdtscope file. Do not forget to add it to your SCM.

Here is how configuration looks with jquery files removed from validation