On the wings of the new rumors that Hulu may extend the length of their commercials to the size of their cable counterparts (that's 5 minute commercial breaks!) I did some digging.
Turns out there is a free app that lets you download Hulu shows as FLV files. It is called StreamTransport and features a split screen with a full functional browser on top and the download button at the bottom. Just navigate to the show you would like to watch and click download.
Now you have a file on your hard drive and whenever there is a commercial you can fast forward through it. Plus it is good of you internet connection is flaky or if Hulu's server is overloaded and slow.
Give it a shot!