I've argued why you should watch The Clone Wars, but watching all 121 episodes, some out of order, is another thing entirely. So to get the best out of your Clone Wars experience, here's the list of essential episodes (plus one movie!) to watch in chronological order.
This story has been updated since its original publication.
The Clone Wars theatrical release
The movie tells the story of Ahsoka becoming an unwilling Anakin's padawan — while the plot itself is nothing groundbreaking, it's a good start to the relationship between the two. It's the only one that's not on Netflix, so it's worth hunting down first.
S3E01: Clone Cadets
The first episode of season 3, Clone Cadets introduces a handful of the clones that we follow through the series, all the way through to Season 6. Seeing as they all essentially look the same, it's good to get a feel for them early.
Oh look, here are those clones again.
S1E09: Cloak of Darkness
As we're skipping the underwhelming first episode, this is a good one to introduce Dooku and his apprentice, Asajj Ventress.
S1E10: Lair of Grievous
Another one that focuses on the baddies, you won't find many of the recurring main characters here, but the dark side machinations are still interesting.
S1E19: Storm over Ryloth
S1E20: Innocents of Ryloth
S1E21: Liberty on Ryloth
This three-parter is both the start of some deeper character development for Ahsoka and a bit more adventure for the clones. One of the characters in this arc is also pretty important if you're planning on watching Rebels later.
S2E01: Holocron Heist
S2E02: Cargo of Doom
S2E03: Children of the Force
Another three-parter that introduces bounty hunter Cad Bane and further builds on the relationship between Ahsoka and Anakin.
S2E18: The Zillo Beast
S2E19: The Zillo Beast Strikes Back
Some people love the Zillo Beast episodes, some people hate them. For me, they're memorable enough to be worth an inclusion.
S2E05: Landing at Point Rain
S2E06: Weapons Factory
This two-parter introduces padawan Barriss Offee — who eventually becomes Ahsoka's friend. It also provides a broader view of the Clone Wars themselves, and includes a little about the relationships between Jedi and their padawans.
S2E07: Legacy of Terror
S2E08: Brain Invaders
Another two-parter that leads on from Weapons Factory, this arc is about brain-invading zombie worms. Other than that, it's mainly worth watching for the moments between Ahsoka and Barriss.
S2E12: The Mandalore Plot
S2E13: Voyage of Temptation
S2E14: Duchess of Mandalore
The Mandalore arc introduces Obi Wan's ex-girlfriend, Satine, who happens to be the Duchess of Mandalore — yes, that place with the armour where Boba Fett comes from. Except for some reason they're pacifists. A good start to the developing Mandalore storyline throughout the series.
S2E20: Death Trap
S2E21: R2 Come Home
S2E22: Lethal Trackdown
These episodes follow young Boba Fett as he sets out to get revenge on Mace Windu — the Jedi who killed his father. Featuring other bounty hunters from the Star Wars canon such as Bossk from Empire Strikes Back and Aurra Sing, the bald, pale bounty hunter with a short cameo in The Phantom Menace.
S3E02: ARC Troopers
This episode continues the story of the clones from Clone Cadets and Rookies — well, some of them, at least.
S1E22: Hostage Crisis
S3E09: Hunt for Ziro
While this Hutt subplot is a little odd (though more so when watched in its original order) it's also more screentime for Cad Bane, and a look at Quinlan Vos, one of the more entertaining members of the Jedi order.
S3E10: Heroes on Both Side
S3E11: Pursuit of Peace
This two-parter is a heavily political one, where Padmé tries to broker peace between the Senate and the Separatists. While it might not appeal to everyone, it's an interesting depiction of grey morality in a universe that loves its blacks and whites.
S3E14: Witches of the Mist
A three-parter that expands on Asajj Ventress, Dooku being a dick and gives us a peek at Darth Maul's people and home planet.
On Mortis: Episodes 15-17 of Season 3 make up the Mortis arc, set on a mysterious planet that exists within the Force. This arc deals with Anakin's role as the 'chosen one' in a less than subtle way, and while I think this arc weakens a lot of other Star Wars lore surrounding the Force and Anakin's prophecy, many Star Wars fans would disagree. Ultimately it's up to you to watch or skip!
S3E18: The Citadel
S3E19: Counter Attack
S3E20: Citadel Rescue
Anakin and Tarkin become bros in one of the series' few nods to the original trilogy. Things also get pretty intense during this high-stakes prison break in/out arc.
S4E07: Darkness on Umbara
S4E08: The General
S4E09: Plan of Dissent
S4E10: Carnage of Krell
A series of clone-centric episodes that have some very illuminating things to say about the state of the Jedi Order. Again, an indicator of the darker direction the series takes.
S4E14: A Friend In Need
This episode re-introduces Ahsoka's low-key love interest, Lux Bonteri, as well as being the first appearance of Satine's sister and important Death Watch member Bo-Katan Kryze.
S4E16: Friends and Enemies
S4E17: The Box
S4E18: Crisis on Naboo
Obi Wan goes undercover with a group of bounty hunters. A lot of it is just him showing off, but the culmination of the arc is a surprisingly intense moment born of Palpatine's plotting.
Two episodes that continue Asajj Ventress's increasingly interesting plotline, as she leaves the dark side behind to form her own morality.
A very surprising return from a film character who really deserved more screen time.
S5E02: A War on Two Fronts
S5E03: Front Runners
S5E04: The Soft War
S5E05: Tipping Points
Ahsoka is sent to train a group of insurgent rebels. Wait, is that really something that's okay for the Jedi to do? Well, apparently yes...
S5E15: Shades of Reason
S5E16: The Lawless
Darth Maul and his brother have some really crazy plans for the world of Mandalore, deciding to capitalise on all that Sith training he has to build a criminal empire. Things get really crazy as the Mandalore plotline winds up.
S5E18: The Jedi Who Knew Too Much
S5E19: To Catch a Jedi
S5E20: The Wrong Jedi
These four episodes are the culmination of Ahsoka's storyline in The Clone Wars, and a really powerful ending to the series (nevermind that there are episodes after it) The sixth season was produced just for Netflix, and mainly consists of tying up previously unclear plot points:
S6E01: The Unknown
"Wait, so if the clones are so loyal to the Jedi, why did Order 66 happen?"
S6E10: The Lost One
"What happened to that Master Sifo-Dyas guy anyway?"
"Why are there so many Force ghosts in the original trilogy but none in the prequels?"
Think I got some of these wrong? Let us know in the comments, I know you will anyway.