the only one I know for sure is that movie 3 is some time after episode 129, since it's the first movie Haibara appears in... the first two are (obviously) before that
the OVA's don't fit into the schedule at all, regardless of release dates... and magic files 2 and 3 are associated with movies 12 and 13, respectively, although I don't think it matters whether they're watched before or after their movie