I use the BlockComment plugin for vim which I mapped to _c and _C to comment an uncomment respectively.
It works really well with the highlighting mode that vim uses. For example, go to the start of a block (function, loop, if statement) then hit Shift-V % to highlight the entire block and then _c to comment it out. Or hit Shift-V 20j to highlight the next 20 lines below the cursor, then hit _c to comment or _C to uncomment.
Oh, and it works for many different languages, not just perl.