Hmm, while browsing things about vim I came upon an excellent article about using vim with perl http://mamchenkov.net/blog/item/vim_for_perl_developers which mentioned a tool to add to your plugins folder (the BlockComment plug-in by Chris Russell). Basically, by highlighting a block of text with your mouse, you can comment that block while preserving its indentations by doing a .c and you can toggle off the comments by highlighting the text and doing .C