These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Accidental Innuendo: We never find out what the book Steve reads in one episode (the book is called "A Really Great Book"), and he's very into it...what is that book about!?
Alternate Character Interpretation: Steve - cheerful inhabitant of a colorful house full of talking objects, or friendless schizophrenic whose loneliness has led him to populate his home with chattering hallucinations?
Awesome Music: You best believe it. And even if you don't much care for music aimed at the six-and-under set, you've got to admit that the show's full of Earworms. The show's theme tune is a good example, and the "Glasses" song from "Magenta Gets Glasses." There was also the "Puppyville" song in Meet Blue's Baby Brother. "Look at all these puppies, this must be Puppyville!"
In a later episode about patience, Joe helps Periwinkle — the neighbor cat — be patient while waiting for a bird's egg to hatch.
What's going to happen to Mailbox when the United States Postal Service finally shuts down? I doubt Steve and Joe would just get rid of him, but there's not going to be much for him to do other than be a big purple lawn ornament...
Franchise Killer: The show has several moments that potentially killed the show. Steve Burns leaving was the first one. For some reason, some parents just didn't find Donovan Patton Adorkable enough. However, the show managed to pull on for another 5 years with Patton as host. The second, more clearer one, was the Spin-Off into Blue's Room in 2006. The many changes made to the spinoff- specifically, non-appearance of many of the cast from the main show and that Blue can now talk, aside from the change to puppetry, gave the franchise one year to live before production of both shows ceased in 2007 and the franchise slowly pattering off into obscurity.
Hilarious in Hindsight: At one point in "Blue's News", Steve and Blue jump into a chalkboard, whereupon Steve grabs a piece of chalk and starts drawing. Steve invented Chalkzone.
Periphery Demographic: The show was surprisingly popular even with older kids and parents—possibly due to a combination of Parental Bonus and the fact that Steve's jokes, while simple enough for kids to understand, weren't so painfully lame as to be unfunny to everyone else.
In fact, most college students will outright admit to watching it, or that was at least true when the show was still regularly airing new episodes, and particularly when Steve was still on.
Replacement Scrappy: Many fans of the show do NOT like Joe. Why? Because he isn't Steve. To be fair, though, he does just as good a job as Steve, he's just a little more enthusiastic about it. It didn't help that the show underwent some major retooling not long after he was cast. Naturally, the actor took the brunt of the backlash despite having nothing to do with, say, live-action puppet sequences.
Rewatch Bonus: Whenever Blue starts up a game of Blue's Clues, if you listen carefully as she proceeds to plant a pawprint on the screen, she is actually saying (or rather, barking) what the answer is.
The episode where Paprika is born has a lot of this. When Steve and Blue find Mr. Salt (who is the first clue), he's pacing while muttering some spice names to himself, as if he's trying to decide on one. Later on, they find that the second clue is Mrs. Pepper, but instead of her being there in person, the clue was on a picture of her. Of course she wouldn't be there; she was busy giving birth!
Tastes Like Diabetes: But it was quite tastefully done for the most part. But then, Blue's Room was created...
They Changed It, Now It Sucks: Though not nearly as discussed as the change from Steve to Joe or to Blue's Room, there was another change that really steamed many long time viewers. Beginning around the middle of the Season 5, specifically in "Blue's Neighborhood Festival," the clues were no longer drawn in the Handy-Dandy Notebook by Joe but instead simply appeared to draw themselves, talked and then sang a little song. Long-timers who stuck around to watch the "Meet Blue's Baby Brother" anniversary special were thrilled that in it, at least, they were actually drawn by Joe and remained silent.
Viewer Gender Confusion: Most of the confusion stems from the lack of Tertiary Sexual Characteristics on Blue; she lacks eye lashes or a slim build as one might expect. She never speaks, just barks, and the pitch is deep enough that it can't be distinguished as explicitly feminine, unlike most cartoon dogs. Also, she is colored (and named) blue, often thought of as a boy's color by many children and parents alike.
It doesn't help that in one episode, Steve refers to Green Puppy (another girl character, and a friend from Blue's school, but voiced by a male voice actor, Adam Peltzman, show headwriter in later seasons) in pronouns twice: once with a male pronoun, and again with a female one. And this was the only indication of Green Puppy's gender for a while.
Anyone else think Periwinkle was a girl when they were a kid?
Magenta is often mistaken as a boy from people who think the show is inverting gender roles. She's just as female as Blue and Green Puppy.
Watch It Stoned: Steve Burns himself joked in a trailer for his Songs for Dustmites album that one third of his periphery demographic fanbase on Blues Clues are stoned college students.