Approval of God: When Christopher Lee came in to record for The Movie, he heard a bit of Corey Burton as Dooku and wondered why he was even needed; Burton was THAT dead-on.
Channel Hop: Due to Disney acquiring Lucasfilm, the series was pulled from Cartoon Network after its fifth season concluded. The sixth and final season wound up on Netflix.
Doing It for the Art: The amount of work put into this series really shows how much the crew cared about it, even just observing from the surface. But when you start noticing and then paying attention to such trivial things like posters on the walls of clone barracks or clubs, the elaborate details on spaceships, bugs crawling around on branches, garbage thrown away on the lower streets of Coruscant, and dozens of other tiny-little back-ground details the creators have sneaked in - despite the fact that most viewers probably wouldn't register any of it the first time viewing - it becomes mind-blowing! Then consider that all of this is made in CGI, with a relatively low-budget when the series was only starting. And when their budget and technological assets increased as the series progressed, they did even more with it.
Going even further, they had assets to use from Lucasfilm's archives. For instance, during the production of Season 3 episode "Wookiee Hunt", the crew had a meeting with Peter Mayhew to make sure they got Chewbacca's appearance (while working within the art style of the show), characterization and body language accurately.
Executive Meddling: George Lucas, being an executive producer, had a say in certain creative decisions (usually for minor things) that would override decisions made by the writers - for instance, it was actually a last-minute suggestion on his part that led to Ziro the Hutt acquiring his speech pattern. Interestingly, it was also Lucas who suggested to design Cad Bane to be Lee Van Cleefin space, and his changes generally didn't interfere with how the stories themselves were told, so it works both ways.
Executive Veto: George Lucas occasionally exercises this power on the show. For instance, the finale of The Lost Missions ends on the planet Korriban - however, the term "Moraband" came up during discussion, and Lucas suggested that it should be the planet's canonical name. A writer later added that "Korriban" is simply an alternative name.
Limited Special Collector's Ultimate Edition: All the individuals Season's DVD and Blu-ray releases contained massive amounts of bonus content, but the Seasons 1-5 Collector's Edition took it even further: it includes the entire series, hours of bonus contents, an episode guide, and the 54-page artbook. And it costs just slightly above the half of the combined cost of the individual Season releases.
Missing Episode: The Clovis arc planned for the fifth season never made it to air. Instead, it was moved to "The Lost Missions" (AKA Season 6).
Never Trust a Trailer: In the trailer for the Season 5 finale, the colour of Anakin's second lightsaber was changed to green so that viewers wouldn't be as likely to suspect that Barriss was behind the Temple bombing.
Official Fan-Submitted Content: The lightsaber technique "Whirlwind of Destiny" used by Petro in "A Test of Strength" was created by nine-year-old Brendon Lake for Hasbro's "Join the Jedi" contest.
The Other Darrin: All characters from the live-action Star Wars movies are voiced by different actors in the Clone Wars series, except for the following ones:
Anthony Daniels returned as C-3PO,
After a few episodes with B.J. Hughes voicing Jar Jar, Ahmed Best returned to the role of the clumsy gungan.
Matthew Wood as General Grievous.
Liam Neeson and Pernilla August reprised their roles as Qui-Gonn Jinn and Shmi Skywalker in "Overlords".
Daniel Logan as Boba Fett and the clone cadets (aside from one who was voiced by Dee Bradley Baker).
Samuel L. Jackson and Christopher Lee reprised their roles as Windu and Dooku respectively in the Pilotmovie before being replaced in the series itself.
After the passing of Ian Abercrombie, Tim Curry takes over as the voice of Chancellor Palpatine.
The Other Marty: When the the three original episodes were edited and released as a feature film, Christopher Lee returned to voice Count Dooku. Corey Burton, who plays Dooku in the ongoing series, had already recorded his lines and Lee re-recorded them, matching his performance to the already-rendered images.
Screwed by the Lawyers: Just like what happened to certain othershows when Disney purchased Marvel, Clone Wars ended up getting cancelled after Disney decided they'd rather invest in their own cartoon. The silver lining though is the remainder of the series will air on Netflix.
Screwed by the Network: Happened to the show during its run on Toonami, when it was suddenly moved from its initial 3:00 AM timeslot down to 5:00 AM.
Short Run in Peru: The bonus content (AKA Season 6) aired in Germany before it aired in the U.S. and Canada on Netflix. 
James Arnold Taylor is voicing Obi-Wan, Plo Koon, Osi Sobeck and Rako Hardeen (both the real one, and while Obi-Wan was posing as him). Hilariously lampshaded in "Counterattack", after Osi Sobeck captured Obi-Wan and his group:
This is exploited in Season 4's Deception arc, where James voices both Obi-Wan and Rako Hardeen (both the disguised Obi-Wan and the real Hardeen). This was a deliberate choice in that since Obi-Wan was undercover as him, Hardeen needed to be voiced by someone familiar enough with playing Obi-Wan's character.
Dee Bradley Baker voices all of the clone troopers as well as Bossk. The former gets taken Up to Eleven during the Umbara arc, where the majority of the dialogue comes from him and Dave Fennoy, Pong Krell's voice actor. In fact, the cast list for "Carnage of Krell" has only three voice actors listed: Baker, Fennoy and Tom Kane (the opening narrator).
Corey Burton voices Cad Bane, Count Dooku and Ziro the Hutt. Narrowly averted between Ziro and Dooku, as while the two of them are both played by Corey Burton in the series, they conversed with each other only in The Movie, in which Christopher Lee returned to play his role as Dooku.
This does happen, however, in "Hostage Crisis" when Cad Bane and Ziro converse after the latter is rescued by the former.
At the end of "A Necessary Bond", Huyang mentioned that the last Jedi youngling who had such an adventure while building his lightsaber was Yoda. Hearing this the younglings immediately started to demand the story, just for Obi-Wan to quickly put them down, telling them that's Another Story for Another Time.
Many haters and even a large numbert of fans were hoping that Ahsoka would eventually die in the series for various reasons (continuity, to give Anakin a huge push towards the Dark Side, etc). In the penultimate episode of the entire series, after her "fate" has already been resolved, a dying Ahsoka appears in a vision for Yoda.
R2-D2's faux Heroic Sacrifice in "Point of No Return" could be seen as this in regards to the fact that characters who appear in Revenge of the Sith or the Original Trilogy can't die in this series. By putting him in the middle of a large colorful explosion that nearly destroyed his body, it's like they said "Sure we can't kill him, but that doesn't mean we can't blow him to pieces". He is promptly salvaged from the wreckage and rebuilt minutes later.
ARC trooper Alpha-17 was going to be a character in the show until George Lucas nixed the idea because it would mean having too many names beginning with A. As a result, we got Rex, who's similar to Alpha, but with a different name.
Plo Koon was originally going to speak only in his Kel Dor language, but it posed problems for him communicating with his fellow troopers, so they decided to have him speak in Basic (the English language of Star Wars).
Mace Windu and Boba Fett's talk in the end of "Lethal Trackdown" was going to be longer, but had to be cut for time, hence why it feels incredibly rushed.
Darth Bane and Revan were to appear in "Ghosts of Mortis", even getting all the way to modeling, but were cut because them appearing as force ghosts seemed counterintuitive to the now established means for how a force user can appear as one.
Originally, at the end of "Carnage of Krell", Captain Rex was originally going to be the one to kill the traitorous General Pong Krell, but ultimately, they decided it didn't fit Rex, so they ultimately had Dogma be the one to pull the trigger.
For a short while the season five finale was intended to end with Ahsoka just going back to the order as if nothing happened but the majority of the writers felt it would be a good time to break away.
Filoni revealed quite a few of these during the 2013 Star Wars Celebration Europe 2:
Writer Brent Friedman also revealed a number of interesting factoids about the planned future episodes for the show on his Twitter.
An arc about a group of soldiers known as "The Bad Batch", which would feature the return of Echo.
Multiple Bounty Hunter arcs were in development.
Captain Rex had a story arc that would involve him being injured.
Another Yoda-centered arc was planned.
A major arc would center around Anakin dealing with Ahsoka's absence.
On the bright side, the Son Of Dathomir comic series and the forthcoming Asajj Ventress novel are signs that the untold tales of The Clone Wars will make it into circulation one way or another. The above events discussed for unproduced episodes will likely be canonized.
The Season 1 episode, The Lair of Grievous, was produced by famous anime studio, Production I.G. The episode won Golden Reel Award, for best sound editing in television animation.
During the Clone Wars panel at the 2010 Comic-Con International, Guinness World Records editor Craig Glenday took the stage to present the series with a certificate proclaiming "The Clone Wars as the highest rated sci-fi animation currently on television".
The title logo at the beginning of "Brothers" and "Revenge" was changed to red, as an homeage to Darth Maul's return.
Similarly, the D-Squad arc episodes had blue logo as an homeage to R2.
Kevin Kiner had flown to Prague and hired a full chez orchestra for the recording of the soundtrack of the four-part Season 5 finale arc, and he did it on his own time, out of his own wallet.
"The Wrong Jedi" is the only episode which ends with a Fade Out, and without the usual ending theme. The latter is replaced by Ahsoka's theme, played by the aformentioned full orchestra.
The series won two-two Daytime Emmy Awards in 2013 and 2014:
Outstanding Special Class Animated Program in both years
David Tennant won "Outstanding Performer in an Animated Program" for his role as Professor Huyang.
Outstanding Individual Achivement in Animation for Christopher Voy, on his work on the animation of "To Catch a Jedi".