I've been singing the praises of Jdownloader
http://jdownloader.org/home/index
There is a new version that has been totally reworked. I had some trouble getting it up, but there is a very good tutorial, and the tech staff is awesome.
By the way, its totally free.
If you have premium accounts, you can preload the logon and password.
You start with a Linkgrabber. When I have a list of links on the page that aren't completely shown, I right click on the link, select copy link, and the clipbopard watcher copies it the the link grabber. It recognizes parts of the same file and groups them together. If there is an archive password, a double click brings up a dialog pass to paste the password. the program also checks to see if the file is available.
If there are several links and the full path is displayed, I just highlight all of them, right click, and copy. The clipboard watcher transers it to the Link Grabber.
It can even read through ProtectLink, Lix, and all the extra text in a list of links in a Rapidshare folder.
Once you're ready, you add the package to the download window. You can watch the download and see if there are any problems with it. Even though I have a Rapidshare premium account, occcasionally something goes wrong and I may get a premature end of file error. All I have to do is right click on that specific piece and reset. It will ask if I want to delete the partial file, and then recycle the file for the next available download slot.
I run 5 parallel downloads at a time. I have broadband, so its no strain.
I also have enabled unpacking and and joining. I could have the program delete the pieces after the file is joined, but I prefer to check before deleting. With the old version I had trouble with some of the joins being defective, and I would have to rejoin.
It even worked well with Mediafire. I often had one out of 6 links give me an error, but I just reset, and voila, I had a movie.
Once the queue is built, I often go to bed and leave it run. A lot of times, even though there are errors, it will still recycle the file and try to redownload.
I delete each container when it is finished. I could set it not delete from the queue until I restarted the program.
Its an amazing piece of software. I tried a number of others, both free and commercial, and nothing came close.