Brother Chuck - If you're not one of the members of the cast of season 3 (aside from the old boss and the old spies) raise your hand.
Hand Wave: Now, if you're not in Season 3 and haven't raised your hand yet, raise it now.
Bland-Name Product - Series 5 had a poltical party called the "Morris Dancing Loony Party". This was based on the 'Monster Raving Loony Party', a joke political party in Britain that used to try and get the votes of people who looked upon the real parties with disdain.
Another episode has "Twitcher", a parody of social networking site Twitter.
"50 Pence" for 50 Cent.
The Cast Showoff - Rachel Petladwala, the actress who plays Rose, got to show off her singing in the Series 1 episode 'Eyes On Their Stars'.
Ben Kerfoot, who plays Oscar Cole, also got to show off his dancing in the Series 5 ep 'Bully Elliot'.
Commie Land - Boldovia in one of the series 3 episodes.(I think. It's a bit more Fascist.)
Cowboy Episode - In "Dark Star", an old enemy of Frank's breaks out of prison and comes gunning for him. Colt Winchester (really Colin from Winchester) and his men have adopted cowboy outfits and affectations and the whole thing plays out like High Noon.
May Contain Evil - Any product SKUL uses as the basis for one if its schemes. Examples include the mind regressing beauty treatment in "Forever Young", the logos that turn kids into human/clothing hybrids in "Evil by Design", and the addictive wursts in "Fit to Wurst" to name a few.
Mr. Fanservice: Notably, Oscar was adored by the fanbase, which probably stemmed from his appearance (tall, lots of blond curly hair, bright blue eyes) and Dark and Troubled Past, which appeared to have affected him in a way that made him completely adorable. Later on, we see that the actor is in fact an extremely good dancer.
Non-Action Guy: Tom, who doesn't accompany Dan and Aneisha on missions.
Offscreen Moment of Awesome - Two in Red Button Rampage. First Blaine knocks unconscious two army men in an enclosed space, off screen, later while the climax is happening an army sergeant is dealing with a squad of reinforcements, we don't see the fight... but she comes back with a handful of dogtags!
Searching the Stalls - One of Colt Winchester's henchmen does this while searching for Frank in the deserted school in "Dark Star". Figuring Frank mus be in the last stall, he burst in. Frank is actually hiding behind the the bathroom, and has rigged the toilet to blow up in the mook's face.
Shoe Phone - Various gadgets disguised as school paraphernalia.
Submarine Pirates - The Octopus from the episode "The Octopus". He uses his submarine Naughty Lass to hijack ships to steal the components he needs to make a nuclear warhead to melt the polar icecaps.