Coffee shop where Shawn, Gus, & Lassiter look at the stuff in the back of Henry's truck in episode #113 "Game, Set… Muuurder?". Also where Shawn fake proposes to Juliet in episode #208 "Rob-a-Bye Baby".
Clinic on Gus's route where Shawn finds him to talk about the case in episode #101 (the pilot).
Cafe where Shawn & Juliet talk in episode #103 "Speak Now or Forever Hold Your Piece". Filmed in the Tramonto restaurant overlooking the marina.
Juliet and Karen Vick join Marlowe and her friend for her Bachelorette party in episode #707 "Deez Nups".
Beach where Juliet and Lassiter talk about the case in episode #105 "9 Lives". Also the beach that young Shawn runs down in his cape at the start of episode #108 "Shawn vs. the Red Phantom" and where nowadays Shawn talks with Talia later in that episode. Where the dead surfer is found in episode #502 "Feet Don't Kill Me Now". Juliet and Rachel chat on the beach in episode #712 "Dead Air".
Coffee shop where Shawn and Gus go to begin their investigation at the beginning of episode #109 "Forget Me Not". Also where Shaun and Gus meet up with Brandon for their fake date in episode #114 "Poker? I Barely Know Her". It is also where an infection occurs in episode #413 "Death is in the Air".
Where Juliet talks to Alice Bundy in episode #115 "Scary Sherry: Bianca's Toast". Also used as an establishing shot in episode #415 "The Head, the Tail, the Whole Damn Episode".
Front entrance to the museum Shawn & Gus visit at the start of episode #610 "Indiana Shawn and the Temple of the Kinda Crappy, Rusty Old Dagger".
Archaeology department where the murder victim worked in episode #202 "65 Million Years Off".
Lab where Dr. Richard Colbert is found dead in episode #305 "Disco Didn't Die. It Was Murdered!".
The group meets with Max The Axe to exchange Herb Pollock for Marlowe in episode #707 "Deez Nups".
Restaurant where Dutch the Clutch jumps off the balcony from in episode #303 "Daredevils!". Also where the Mr. Yang clue is left near the beginning of episode #316 "An Evening with Mr. Yang".
Dock where Henry keeps his boat in episode #310 "Six Feet Under the Sea". Also the dock where Lassiter & Juliet go to try and get a boat to hunt the shark and where Shawn & Gus leave with the fisherman in episode #415 "The Head, the Tail, the Whole Damn Episode".
Camp where the pool scene from episode #315 "Tuesday the 17th" take place. This pool has since been removed.
Street (just outside the entrance to the park) where Juliet and Lassiter pull over the wrong car in episode #513 "We'd Like to Thank the Academy".
Area where Shawn and Gus go through the SBPD obstacle course & shooting gallery in episode #513 "We'd Like to Thank the Academy".
Exterior of For Nicholas Army base in episode #410 "You Can't Handle This Episode".
Shawn and Gus arrive at the prison for Jack Atwater's transfer back to police custody only to see him shot in episode #701 "Santabarbaratown 2".
The Psych team sees one of the actors with the director beneath the theatre in episode #715 "Psych the Musical".
Shawn and Gus are driven into the base by Ewan O'Hara in episode #410 "You Can't Handle This Episode".
The team talk to the head of the mental institution after a patient escapes in episode #715 "Psych the Musical".
Industrial area where Mr. Yin leads the team and captures Juliet in episode #416 "Mr. Yin Presents".
Warehouse where Mr. Yin draws Mary and later the team in episode #416 "Mr. Yin Presents". (I'm fairly certain this is here)
Woody answer's Shawn call in his trailer which is parked in a sketchy industrial area and not the beach in episode #709 "Juliet Wears the Pantsuit".
Movie theater where Shawn pretends to see "The Little Mermaid" in the intro of episode #416 "Mr. Yin Presents".
Juliet goes on a date with Lordan as part of the sting when she is confronted by Gus in episode #702 "Juliet Takes a Luvvah".
Law firm that Shawn and Gus follow Toby Shore from, then chase him while wearing silly costumes in episode #503 "Not Even Close…Encounters".
Shawn stands outside the hospital concerned for father only to encounter Chelsea trolling for elderly hotties in episode #701 "Santabarbaratown 2".
Theatre where the first murder of the episode takes place in episode #504 "Chivalry Is Not Dead…But Someone Is".
Lloyd brings Henry to the airport, where they take off in a small plane while being pursued by gunmen in episode #704 "No Country for Two Old Men".
Shawn and Gus go to pick up Rita Quinn at the airport, and later they stop Leo Quinn from fleeing in episode #714 "No Trout About It".
Henry goes to pick up a package for Juliet's step-father Lloyd and his attacked by some thugs in episode #704 "No Country for Two Old Men".
Henry and Lloyd stop briefly in an alley after escaping some gunmen in episode #704 "No Country for Two Old Men".
Shawn, Gus, and Juliet talk to the Mexican Police about the kidnapping of Henry and Lloyd in episode #704 "No Country for Two Old Men".