The title of this episode "2001" and the Season 4 episode 2010 (2001) (part of the same story arc) are titles of two Arthur C. Clarke novels, both of which were also made into films.
When Senator Robert Kinsey storms out of the Gate Room after Major Carter returns, Col. O'Neill tells Kinsey, "That's O'Neill... with 2 Ls!", which he 'expresses' by holding up his first THREE (3) fingers; thereby asking Kinsey...and us the viewer...to 'read between the lines'. ;)
After O'Neill and Carter return from their first round of negotiations with the Aschen, they are in the control room with General Hammond. They are talking about the note that was sent through the Stargate from Col. O'Neill from the future.
In the background, Sgt. Walter Harriman is holding and presumably drinking from a bottle of Pepto Bismol (easy to determine from the shape and color of the pink bottle). It must have been a rough day of shooting.
When the Aschen share the idea behind their bioweapon, they say it can be targeted towards the specific DNA of the enemy. This would mean the Goa'uld symbiotes. In 2010 (2001), Teal'c mentions not many Jaffa are loyal to Earth after the war. One can speculate that the weapon was indeed used in that timeline, thus killing all the symbiotes and any Jaffa carrying them. Such an action would cause animosity since Earth was essentially willing to commit genocide to destroy the Goa'uld.
When Senator Kinsey first refers to Jack in the limo he said "Colonel Starsky or is it Hutch, I can never remember which one you are" A direct reference to Chain Reaction (2000) where Jack teams up with Maybourne.