The name of Gil Bates is a play on words of Bill Gates. Both, real and fictional, are geniuses of informatics and computers.
When Bones tells Booth about getting Brainy Smurf from Andy Pfleuger she states he is the Lacrosse captain. Yet in season 5 at her school reunion Andy Pfleuger is very nerdy and states he spent a lot of time in wood shop.
The date of the drug bust, June 12, 1987, is the same day Reagan gave the, "tear down this wall" speech.
The Amiga used 3.5" floppy disks, not the 5.25" one used in this episode.
Patrick Fischler, who plays Gil Bates, also featured in an episode (S4 E19) of David Boreanaz's previous show, Angel.