This extension warns you when Hulu ads are over
This extension will add a text input box right beside the search box in every hulu.com page.
To use, when an ad comes, just copy the amount of seconds left in the ad in the box and hit return [See screenshot 1].
Mute the sound if you wish, and go do whatever you like, an alert will notify you when the time is done, un-mute the volume [See screenshot 2].
Since there might not be a way to actually skip the ads, I guess this is the second best.