My favorite switch is -l, and this is why:
perl -i.bak -ple 'BEGIN{$/="\n"}'
gets you from Unix to DOS (or should) and changing "\n" to "\r\n" gets you back.

Update: assuming you're always converting to the system you run the command on, that is--the -l flag gives you native line-endings.

Though of course if you're in MSDOS, you presumably need to fiddle with the quotes some.