Unfortunately, you are out of luck here, mate. Totally, speaking that is.
You won't find an all-in-one solution that handles it all. Some have a queue system but are broke (as Youtube changes it's steaming mechanism). Some that do, only download FLV files. One decent one I saw (Youtube Downloader HD, link below) has all the options with support of upto 720p videos, but it can't differentiate between them. You can't auto set it to download the best quality video (HD, MP4, hi-res FLV, and low-rs FLV). And to top it off, you have to insert one video link in at a time.
There was another one Tomato Youtube Downloader, which had a half decent interface, but it always got stuck at 50-80%, and has no option to pause or resume the download.
I know, big mess. Try this one out for the time being. It's free:
Youtube Downloader HD - Download and Convert Online Video - Free