Is there any way to skip some Java files when compiling under Eclipse?
There's another way to do it. I discovered it by first using the Build Path -> Exclude option in other answers, as Eclipse said something about configuring filters.
Right click the project -> click Properties -> click Java Build Path -> click Source tab -> select ProjectName/src -> click Edit... (or double click Excluded) -> add an Exclusion pattern like com/blah/blah/blah/, potentially with wildcards.
It looks like the wildcards are your standard * and ?, but they also have **, which appears to be for wildcarding any number of folders, which must imply that * and ? are for only wildcarding a single file/folder name.