Red John's last appearance, where he talks down to Jane and tries to kill him, only for Jane to gain the upper hand and kill him as he resorts to pleading to live. Sounds a lot like Percy's death, especially since Xander Berkeley played both characters.
Also, since Lisbon (Robin Tunney) is best known for being Sarah in The Craft, the whole episode "Red Rum" had a bit of this. And Lisbon's crazy looked remarkably Tourette's-ish, Tunney's other major role being the lead in Niagara, Niagara.
Jane commenting "You should have seen me ten years ago" might be a Shout-Out to Simon Baker's 2001 drama series, The Guardian.
Christina Cox, of Nikki & Nora cult fame, turns up as a girlfriend in the same episode.
John Billingsley (Dr. Phlox) and Connor Trineer (Charles "Trip" Tucker) guest-starred together in the 11/18 episode "Red Moon."
And Hoshi consulted with the CBI (ep 3x12).
The show is loaded with former 24 cast members. Just a couple examples are Gregory Itzen (Charles Logan) as Virgil Minelli and Leslie Hope (Teri Bauer) as Kristina Frye. Carlo Rota (Morris, Chloe's husband) also appears as a Russian red herring suspect named Dimitri Zubov.
Morena Baccarin (a.k.a. Anna, Inara, Adria) is a matchmaker, recently widowed, in the episode "Every Rose Has Its Thorn."
Sid Hammerback lost his job at CSI: New York and he now harvest organs for the bad guys.
The Other Darrin: One of the biggest challenges for fans trying to figure out who he is, is the fact that Red John made appearances before the actor who plays him was cast. Like Sylar on Heroes, they were played by various stunt doubles and extras. As a result some of his earliest appearances, like in "His Red Right Hand", he doesn't resemble any of the final suspects. In "Red John's Friends", Red John IM's Lisbon's team. The person typing in real life was Simon Baker, leading many to believe that Patrick Jane was Red John.
Real-Life Relative: Simon Baker's, Tim Kang's and Owain Yeoman's wives have all appeared on the show.
Screwed by the Network: Fans have been accusing CBS of this since Season 5. First they put the series in a graveyard shift (10 PM Sunday), then every so often they force it to compete with football and other highly-rated shows. At the same time, the series itself has seen its share of critics increasing since Season 4, who accuse the writers of pulling The Chris Carter Effect with its Red John Myth Arc.