Best episodes?

How long of a list are you looking for? As a good portion of the show focuses on those things, a comprehensive list is going to be rather long. Especially so, considering the episodes are rarely single self-contained stories, and are usually part of story arcs 3-4 episodes long. With those things in mind here is my list of good episodes, and those that center on Anakin, Obi-Wan, and Ahsoka, broken up by arcs (the list will be in chronological order, not the order they aired, by the way):

1x02 Rising Malevolence
1x03 Shadow of Malevolence
1x04 Destroy Malevolence (Anakin, Ahsoka, and Obi-Wan on an early mission toghther)

1x06 Downfall of a Droid
1x07 Duel of the Droids (Anakin and Ahsoka in these 2. Good look at the early part of their relationship)

1x09 Cloak of Darkness (An early Ahsoka-centric episode, not sure you wanted episodes that developed her character, but I included a few anyway)

1x13 Jedi Crash
1x14 Defenders of Peace (Some more Anakin and Ahsoka together)

1x17 Blue Shadow Virus
1x18 Mystery of a Thousand Moons (1x17 isn't so great, but it sets up 1x18 which has some good Anakin/Obi-Wan and Anakin/Ahsoka stuff)

1x19 Storm over Ryloth (Good Anakin and Ahsoka centric episode, should have quite a bit of what you're looking for)

2x01 Holocron Heist
2x02 Cargo of Doom
2x03 Children of the Force (Same here, Anakin, Ahsoka and Obi-Wan all feature prominently in this good arc)

2x05 Landing at Point Rain
2x06 Weapons Factory
2x07 Legacy of Terror
2x08 Brain Invaders (This nice 4 episode long story I think offers quite a bit of what you're looking for)

2x11 Lightsaber Lost (Another good Ahsoka-centric episode)

2x12 The Mandalore Plot
2x13 Voyage of Temptation (Obi-Wan centric story, some good moments with him in Anakin in 2x13, along with a great foreshadowing scene near the end)

3x02 ARC Troopers (Good Anakin/Obi-Wan episode)

3x07 Assassin
1x22 Hostage Crisis
3x09 Hunt for Ziro (Not great, but has moments from all 3 characters)

3x15 Overlords
3x16 Altar of Mortis
3x17 Ghosts of Mortis (Some people think otherwise, but I think this is an excellent arc, with a lot of character development to offer Anakin, Ahsoka, and Obi-Wan)

3x18 The Citadel
3x19 Counter Attack
3x20 Citadel Rescue (Anakin, Ahsoka, and Obi-Wan on another mission)

3x21 Padawan Lost
3x22 Wookiee Hunt (Ahsoka-centric, but has a lot to say about Anakin/Ahsoka's relationship)

4x07 Darkness on Umbara
4x08 The General
4x09 Plan of Dissent
4x10 Carnage of Krell (None of the major characters feature prominently in these 4 episodes, but I included them because it is considered, correctly, to be one of the best arcs in the series)

4x11 Kidnapped
4x12 Slaves of the Republic
4x13 Escape from Kadavo (Another nice story arc with Anakin, Ahsoka, and Obi-Wan working together)

4x14 A Friend In Need (Another good Ahsoka-centric episode)

4x15 Deception
4x16 Friends and Enemies
4x17 The Box
4x18 Crisis on Naboo (Obi-Wan centric, but adds quite a bit too Anakin's character as well. 4x17 is a little mediocre, but the others are good, in my opinion)

4x21 Brothers
4x22 Revenge
5x01 Revival
5x14 Eminence
5x15 Shades of Reason
5x16 The Lawless (While Obi-Wan is featured prominently is these episodes, I'm not sure they match exactly with what you're looking for. I included them, because like the other one earlier, this is one of the series best arcs)

5x17 Sabotage
5x18 The Jedi Who Knew Too Much
5x19 To Catch a Jedi
5x20 The Wrong Jedi (Another one of the series best few episodes, these include a lot of what you're looking for, especially Anakin/Ahsoka)

I'm not sure if you've seen the show, but if you have, you can go ahead and ignore my notes in the parentheses. If this list is too long I might be able to trim some episodes off, and if you want more I can probably add some too.

That's the best list I can think of right now, if anyone else thinks I overlooked something, feel free to correct me.

That's a neat list! I have seen the show myself, but I have forgotten most of it. I only remember the biggest moments so I needed some help with this. The list is quite long though, but I have something to work with now! So thanks for your effort (y)