I configured my Force.com project in Eclipse to download ALL standard and custom objects, but it skipped some, e.g. it didn't download CaseTeam, CaseCommnet, EmailMessage, etc. - at first I thought maybe because these are "subobjects" of "Case", but then why did it download "CaseMilestone"? I don't get it. Similarly, there's a WF rule on CaseComment, which also didn't get downloaded.
I wanted to be able to download ALL the metadata of an org to check into source control to save the state of the org for rollback purposes - is that not possible? Do I really need to manually restore some parts of the org that are not downloadable via the metadata API?