Since the studio had such a long run, I'll split some of these up by decade. In fairness, I haven't seen every single H-B show ever produced. I don't think I could stomach that. But these answers will be based on what I'm familiar with.
Favorite Hanna-Barbera show?
'50s/'60s: Pretty much everything from The Huckleberry Hound Show through The Jetsons.
'70s: Not the best decade for the studio, but Hong Kong Phooey, and if I'm in the right mood, anyone of the Scooby shows. I love just how unintentionally bizarre "The New Scooby-Doo Movies" (the version with animated celebrities) was. And Dynomutt had a fun premise.
'80s: Probably "Yogi's Treasure Hunt." It was a rare instance in which a revival of H-B's classic characters worked well, and was written by folks who clearly grew up with, and understood the characters. And again, more so for the strangeness, but I have a slight fondness for some of the cartoons spinoffs of live action properties - specifically "The Fonz and the Happy Days Gang" and "The Little Rascals." Not classics by any means, but pleasant half hour killers. Scooby-Doo picked up quite a bit of steam towards the end of be '80s, especially with "A Pup named Scooby-Doo."
'90s: Don't know if I want to count those early Cartoon Network shows. Umm... Let's see... That "Fender Bender 500" segment on "Wake, Rattle, and Roll" was kind of fun.
Least favorite show by the two?
'50s/'60s: Ruff and Reddy (or as I like to call it, "Ruff and Not-Quite-Reddy"), The Petet Potamus Show, the Abbott and Costello and Laurel and Hardy cartoon adaptations, the Banana Splits... The action-adventure stuff aren't "least favorites" per se, just not my cup of tea.
'70s: Most of them! Notable ones - the non-Space Race segments on "Yogi's Space Race" ("Galaxy Goof Ups," "Buford," "Galloping Ghost"), "Casper and the Angels," the Scooby copies ("Goober and the Ghost Chasers" in particular).
'80s: The seven minute "Scooby and Scrappy" shorts, the Mork and Mindy cartoon (I mentioned before that I only liked "some" of these spinoffs!), "Pink Panther and Sons" (save for that catchy '80s theme song).
'90s: Need to see more from this era.
Favorite character/characters?
See number one. I also have a fondness for anxiety-filled characters like Hardy Har Har and Zilly (from the "Dastardly/Muttley" series). Also Ricochet Rabbit's buddy Droop-a-Long.
Least favorite character or characters? An obscure one, but those three bear cubs from the TV movie "Yogi's Great Escape." Not to mention the Boo Brothers and Flim-Flam, Bogle and Weerd ("13 Ghosts of Scooby-Doo.")
Pixie, Dixie, or Mr. Jinx? Like, uh, ya know, I was like always kinda partial to Mr. Jinx