My '98 Forester runs perfect for the most part. However a problem started this summer. After close to an 30-45 minutes of driving, the check engine light comes on, complete loss of power and stalls at lights and such. If I let it sit for 30 minutes or so it runs perfect again. Any ideas?

That could be anything.

One way to know for sure is to get a scan tool and check what error code you got.

mmmm...30-45 minutes od driving = starting to overheat = power loss......
cooling for 30 minutes = not overheating.....check the coolant resevoir for bubbles while the car is warm.....possible leaking headgasket...not quite blown but gettin there!!!

better scenario is a stupid a$$ sensor is heating up and then begins to go haywire....O2 sensor acting up....alll guesses...but like Alex said the scan tool will tell no lies!!

RS TURBO might be onto something... Blown headgaskets are a known problem on the MY98 Foresters.