I think if you click on the project node in the Project Explorer and press F5 or right click and select Refresh, all resources for that project will be refreshed. Also, if you CTRL+click on multiple projects, you should be able to refresh multiple projects at the same time.
A single click on a project, a CTRL+A to select everything, and an F5 should do exactly what you need - refresh everything.
I'll have to test this when I get the chance, but I believe this is how I overcame similar problems in the past.
I've noticed that this answer routinely is getting down voted. I'd like to point out that the question refers to a specific version of Eclipse: 3.4.2. There was actually no automatic method to refresh out-of-sync resources until version 3.7 Indigo of Eclipse, as mentioned in James Blackburn's answer. The method described in this answer is the only method to achieve this in version 3.4.2 (and any other version before 3.7 Indigo).
