Portal/HL Story crossover
The Borealis, the ship where you have to go in HL3/episode 3, to destroy the microchip, belongs to Aperture Science...
At the end of HL2 episode 2 you can see the Aperture Science Brand on a container at the borealis. Dr. Kleiner talks about Aperture Science....
So...
I must agree with your theory. I just had the same. So I googled it, and found this thread. I think the GMan is Cave Johnson, who is trying to fix his fail in the past - beeing contaminated (is this the right word?^^ my english is not so good) with mercury. He invented GLaDOS >while< he was...