Most people viewing this forum will probably already know this, but I'm posting it anyways. The LEGO Island Comic Adventures were originally on the LEGO website, but removed with the rest of the LEGO Island portion. However, JrMasterModelBuilder recovered the files from the developer's website!
http://tinyurl.com/legoislandcomicadventures
(EDIT: For some reason when I put the Mediafire link in directly the link got screwed up, so I have to use tinyurl. It just redirects to the Mediafire download.)
Enjoy! It also includes the Alpha Team comics and the Minifig Handbook, which has some LEGO Island story stuff.
Now, here's something that isn't quite LEGO Island, but obviously a throwback to it.
http://city.lego.com/en-us/applications/trainstory.aspx
It's a LEGO interactive comic game thingy that was added to the site sometime last year. It's not totally LEGO Island, but there are many references to it (A kid that looks like Pepper on a skateboard stopping a robber is too close to be coincidence).