Daniel Jackson makes a sarcastic remark about how they can defeat the Goa'uld by uploading a virus into the mothership. This is a reference to Independence Day (1996), which like Stargate (1994), was written by Dean Devlin and Roland Emmerich and directed by Emmerich.
When Senator Kinsey asks Colonel O'Neill if he's ever seen a Goa'uld starship, he responds that he has. Immediately following his remark, there's a scene of a ship landing on top of a pyramid. This is footage lifted directly from Stargate (1994).
In the 44:12 runtime, there is 15:22 of clips.
The Pentagon refers to the Stargate program as "Area 52".
The episode is reminiscent of the Robertson panel, which ostensibly was formed by the US government to determine whether UFOs should become a subject of serious scientific inquiry, or were a threat to national security. Before the panel had even made any conclusions, the head of the panel, Howard Robertson, had stated that he personally felt there was nothing to UFOs. Many UFO enthusiasts and scientists, even those scientists within the Robertson Panel itself, felt he was biased against studying UFOs from the beginning, and was only put in charge to quash any serious scientific studies being conducted, much like Senator Kinsey having all but made up his mind about the Stargate program before he even came to Stargate Command.