Vim should detect whether to use set fileformat=dos or fileformat=unix, unless the lines are not delimited consistently.

I tend to use perl to make these kind of code changes, e.g.
perl -pi -e ‘s/\r$// *.sql
also pretty useful for any other global search/replace problems you might have.

The svn:eol-style property in Subversion sounds promising. I wonder just how well it copes well inconsistent end of line delimiters – hopefully better than vim!