The Clone Wars
S1E9 - Cloak of Darkness
This is a great episode that features Ahsoka Tano, Jedi Master Luminara Unduli, and Asajj Ventress.
S1E22 - Hostage Crisis
Anakin takes on a group of bounty hunters including Cad Bane who have taken over the senate building.
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S2E4 - Senate Spy
Some interesting drama between Anakin, Padme, and a former acquaintance of hers.
S2E10 - The Deserter
Insightful look into clones and choices.
S2E11 - Lightsaber Lost
A fun Ahsoka Tano episode.
S2E13 - The Mandalore Plot
S2E14 - Voyage of Temptation
S2E15 - Duchess of Mandalore
A trilogy of episodes full of important information regarding Obi-Wan and the Mandalorians. These are some of my favorite episodes.
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S3E9 Hunt for Ziro
More Cad Bane and Quinlan Vos.
S3E12 Nightsisters
S3E13 Monster
S3E14 Witches of the Mist
Another trilogy of episodes that take a look into Count Dooku, Asajj Ventress, and her home world.
S3E15 Overlords
S3E16 Altar of Mortis
S3E17 Ghosts of Mortis
A three episode arc that deals with Anakin, the prophecy of the chosen one, and impactful information down the line for the Rebels animated series.
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S4E7 Darkness on Umbara
S4E8 The General
S4E9 Plan of Dissent
S4E10 Carnage of Krell
A four part story focusing on clones that raises more thought provoking questions regarding their roles, personal identities, and freedom.
S4E21 Brothers
S4E22 Revenge
An important character returns.
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S5E14 Eminence
S5E15 Shades of Reason
S5E16 The Lawless
An impactful group of episodes for multiple characters and storylines. A must see in my opinion.
S5E17 Sabotage
S5E18 The Jedi Who Knew Too Much
S5E19 To Catch A Jedi
S5E20 The Wrong Jedi
The Jedi must solve the mystery of a terrorist bombing at the Jedi temple. These are my very favorite episodes of the entire series.
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S6E1 Unknown
S6E2 Conspiracy
S6E3 Fugitive
S6E4 Orders
More information on Order 66.
S6E10 The Lost Ones
Who was Sifo-Dyas?
S6E11 Voices
S6E12 Destiny
S6E13 Sacrifice
Yoda goes on a journey to learn more about the Force.
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S7E9 Old Friends Not forgotten
S7E10 The Phantom Apprentice
S7E11 Shattered
S7E12 Victory and Death
The Ahsoka and Mandalorian plotlines collide with events from Revenge of the Sith.