JDownloader is a JAVA based tool that works on Windows, Mac, and even Linux. This tool completely automates the downloading process from popular downloading sites such as (RapidShare and MegaUpload) and makes them more tolerable. You can feed links, or you can add links for multi-part downloads and insert them into JDownloader and it will automate the process, tweak wait times, auto-recoonect if you happen to get disconnected, or you can even set a schedule on it.
JDownloader works on a stand-alone application or you can integrate it into FireFox with the popular FlashGot extension.