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.
Bellisario's Maxim: Not everything about this computer world really makes sense as related to how we use computers. It is just an interesting setting, as well as way to bypass fan comments related to the computer limitations. Like "Why are there no shadows?" "Uh...It's inside a computer!"
Hexadecimal: Nevermind, it will be glorious!
Cliché Storm: Certain episodes have their plot built on a long string of cliches, but it is either done as an Affectionate Parody or otherwise knows what it is doing.
Epic Riff: The episode dealing with Enzo's birthday sees Megabyte roll up with an electric guitar and play an absolutely face-melting solo. It then turns into a Power of Rock showdown between him and Bob for even more epic.
Epileptic Trees: Quite a few fans like to believe that Megabyte and Hexadecimal merging is what caused Megabyte to become more vile, crazy, and dangerous later in the series. It would certainly explain the stark contrast between "give Enzo a guitar" Megabyte of season 1 and "try to commit genocide" Megabyte of season 3 but that's about the extent to which it makes sense.
"Funny Aneurysm" Moment: Megabyte and Matrix's brutal fight at the end of season 3 makes the earlier moment where Megabyte gives Enzo a guitar for his birthday seem a lot less funny than it originally was.
Genius Bonus: The more you know about computer hardware, computer software, computer programming and CGI the more entertaining the show becomes. Several character's names are rooted in technical terminology. In particular the character designs for Phong (phong shading) and Ray Tracer (Ray Tracing) actually demonstrate the CG principles they are referencing.
There are a few, mostly relating to binomial sequences. The punchline to one joke is told in binary and when Daemon orders Deacon to recite Code 101. He proceeds to recite a series of binomial numbers; the code translates to five, four, three, two, one, zero.
Growing the Beard: The first two seasons were fun and entertaining, but excessively hampered by Moral Guardians that hindered the growth of a more mature show, they weren't allowed to cut to a commercial with someone in immediate peril (like falling off a cliff) for fear of upsetting the children. The final four episodes of the second season started up some more thematically interesting stories with a continuing storyline that fed through the rest of the series, which really hit its' stride in the first few episodes of the virtually censor-free third season.
Nintendo announced that their next console would be called the "Nintendo GameCube." The fact that the console's default color was purple did not hurt.
Mouse: "Wow! Now THAT'S what I call a bug zapper!"
Dot: "I don't believe it! We've been saved by a game cube!
Another episode featured a brief gag (aired in 1997) that had a battleship called the SS Cameron catching fire and sinking. This was in reference to the obscenely overbudget fiasco of Titanic and what people were predicting of James Cameron's career...
The number of VA's Reboot has in common with Adventuresof Sonic The Hedgehog. In particular, for the first two seasons, Hack and Slash were played by the same actors who played Scratch and Grounder, also inept villainous robot mooks.
Hype Backlash: The fourth season came out after being uncanceled three years after the third season. With all the Fan Fiction and rampant Wild Mass Guessing from the fandom (with no expectation of ever getting a resolution), there were bound to be a few accurate theories and a few fanfics that proved to be a more satisfying conclusion for the Daemon arc.
Jerkass Ball: How some of the characters (particularly Dot, though she has a My God, What Have I Done? moment when she finds out the truth) treated "Glitch" Bob when they thought he was a copy. Notably, AndrAIa and little Enzo avert this.
Seasonal Rot: Season 4 is not well-liked, particularly the "My Two Bobs" arc (originally broadcast as a single TV movie).
Although, as always, YMMV. The "Daemon Rising" arc is fairly popular with some fans.
Seinfeld Is Unfunny: The CGI itself. It was mind blowingly cool when the show first premiered but was still very stilted and awkward because of the technical limitations. It didn't help that Toy Story premiered the following year with a film budget and time table that made some people believe that ReBoot was a cheap, inferior CGI product. This is in addition to the rampant Executive Meddling that hampered the show. The truth is that this show and Beast Wars laid the groundwork for CGI television and regardless of the technical limitations the story and scripting was of excellent quality.
In one episode the Binomes try to win the game for Bob by triggering an Earth-Shattering Kaboom, while still inside the planet. Bob was not amused.
"I'm supposed to save them from the User, not themselves."
In another episode, the entire population except Enzo was rendered stupid. Cue a game. Enzo finally discovers the optimum plan: Tell them the User needs their help more.
"We are helping! We are helping!"
Took a Level in Badass: Clearly Matrix, but also backup/little Enzo. He berates infected Matrix in particular, and infected AndrAIa by extension. Guy's got some damn big nodes to chew out his alternate self.
backup Enzo: You'd hurt our dog?
Uncanny Valley: Hex's Dot impression in the video game looks right, but maintains or even exaggerates Hex's signature walk with the swinging arms and the sashaying hips. Fetish Fuel turns into Nightmare Fuel when Hex's mask is removed in the form of Bob pulling off Dot's face, complete with squick sound effects.
Visual Effects of Awesome: At the time, at least, pretty much every part of Reboot was this. Now, not so much. Several of the models still hold up well though, at least when they aren't moving.