Try putting an ‘!’ mark in front of the pattern you don’t want to match – putting
!*.cgi, !*.pm, !*.sql
in the File name patterns section is doing the job in a test I’m doing with Eclipse 3.4.1 (when the pattern was just * there was a file of each type, with that pattern, it is only returning js and pl files).
I was afraid that it would be a bit naive with the patterns and just allow anything that matched one of them to succeed (ie an sql file would match !*.cgi), but this doesn’t seem to be the case.