Here's a little program I use to manage my rapidshare/megaupload downloads...

its called 'Jdownloader' it runs using the Java console (download for free from Sun Microsystems)

all you have to do is copy the links into the 'add links' section, choose where you're gonna save the files (also includes an auto-extract function using winrar and supports rar-passwords) then click start and it'll automatically download your links! easy-peasy

if you need help search google, there's a support section on a few websites (or pm me)

enjoy!