By the whole "99999..." the announcer says its not clear, some say its 50 years from Portal 1 which happened either during/after the Combine invasion or near HL2, so its under half a century after Gordon returns. If we're going with the long route the announcer during the intro says you been sleeping for "9999999", 9,999,999 days is approximately 27,397 years and 3 months. I know Portal is a joke game and the "science" its just for show but that number its ludicrous, the pyramids are only a little over 4000 years old, built of solid stone and even those are falling apart. The aperture labs wouldn't not last even half a millennium, so I'm going with hundreds of years if not even less. I think they went with the 999... thing as a joke to show that a lot of time has passed but that the relaxation system is breaking down and can't keep track anymore.