Where: Smallville (TV series)
Comics: Warrior Angel, Fantasy Comics Featuring Warrior Angel
Creator: ?
Company: Fantasy Comics

Since it would make little sense to have DC Comics within a DC series and they'd want to avoid showing rival companies' comics, Smallville featured the fictional comic Warrior Angel across multiple episodes, showing too many issue covers for me to include them all here.

Where: Fringe (TV series)
Comics: Crisis on Infinite Earths, Superman: The Man of Steel Returns, Red Lantern co-starring Red Arrow, Batman, Justice League
Creators: Presumably the same as in our universe
Company: DC Comics

You might reasonably be thinking "hang on, most of these comics exist. Why list them as comics that don't exist?" And that's because while these are real titles for the most part (Red Lantern notwithstanding), these are the parallel universe versions from the TV show Fringe, in a timeline where things went a little differently both in the real world and the comics...

Where: Hellboy (movie)
Comic: Hellboy
Creators: Mike Mignola
Company: Dark Horse Comics

Another case of "but this comic does exist!" Yep, the title does, but not this issue, which was created purely to be an in-universe version of the comic in del Toro's 2004 Hellboy movie.

Where: Dragnet (1967 series), Season 3, Episode 21: Burglary, DR-31
Comics: Commander Jupiter, Wizard Boy, Super Flame.
    Full disclosure - some of these may be movie serials or characters in the comics but not the titles, as there's also Captain Lighting versus the Martian Devils, which is definitely a serial, by Continental Pictures.
Creator: ?
Company: ?

Per IMDB: Several stores report theft of comic books, posters, and pictures about superheroes. 

Where: Gortimer Gibbon's Life on Normal Street, episode 2.7 "Gortimer vs. the Friendship Bro-clet." 
Comic: White Hat
Creator: ?
Company: ? We see a logo, but it's hard to make out.
Mentioned as a comic he likes by the titular Gortimer, and then seen at the end of the episode. White Hat is apparently Phineas Elkstein (sp?), a genius inventor who has to wear a special hat to prevent himself hearing the thoughts of others. There have been at least three movies about the character, the third of which is titled Return of Porkpie (no mention of White Hat in the title), where White Hat and Porkpie battle evil robot mannequins called Mannekills; the heroes throw their hats and the brim blades cut off all the robots' heads. 

Update: In a later episode, Gortimer vs White Hat, Gortimer finds himself transported into an episode of the White Hat TV series, a clear pastiche of the 1960s Batman series given that the fight scenes are accompanied by visible sound effects and that at one point White Hat and Gortimer climb the side of a building in the exact same way Batman and Robin used to:


The TV show also reveals that he has an assistant called Margaret (pictured alongside White Hat), and a nemesis called Green Beret.