As listed in “Star Wars: The Clone Wars Episode Guide” published by DK. You can also see the start of the list explained on the sw.com Blog. The ordering of the Lost Missions are according to Leland Chee on Twitter (thanks to trackofalljades for the heads up).

Cat and Mouse (S216)
Hidden Enemy (S116)
The Movie
Clone Cadets (S301)
Supply Lines (S303)
Ambush (S101)
Rising Malevolence (S102)
Shadow of Malevolence (S103)
Destroy Malevolence (S104)
Rookies (S105)
Downfall of a Droid (S106)
Duel of the Droids (S107)
Bombad Jedi (S108)
Cloak of Darkness (S109)
Lair of Grievous (S110)
Dooku Captured (S111)
The Gungan General (S112)
Jedi Crash (S113)
Defenders of Peace (S114)
Trespass (S115)
Blue Shadow Virus (S117)
Mystery of a Thousand Moons (S118)
Storm over Ryloth (S119)
Innocents of Ryloth (S120)
Liberty on Ryloth (S121)
Holocron Heist (S201)
Cargo of Doom (S202)
Children of the Force (S203)
Bounty Hunters (S217)
The Zillo Beast (S218)
The Zillo Beast Strikes Back (S219)
Senate Spy (S204)
Landing at Point Rain (S205)
Weapons Factory (S206)
Legacy of Terror (S207)
Brain Invaders (S208)
Grievous Intrigue (S209)
The Deserter (S210)
Lightsaber Lost (S211)
The Mandalore Plot (S212)
Voyage of Temptation (S213)
Duchess of Mandalore (S214)
Death Trap (S220)
R2 Come Home (S221)
Lethal Trackdown (S222)
Corruption (S305)
The Academy (S306)
Assassin (S307)
ARC Troopers (S302)
Sphere of Influence (S304)
Evil Plans (S308)
Hostage Crisis (S122)
Hunt for Ziro (S309)
Heroes on Both Sides (S310)
Pursuit of Peace (S311)
Senate Murders (S215)
Nightsisters (S312)
Monster (S313)
Witches of the Mist (S314)
Overlords (S315)
Altar of Mortis (S316)
Ghosts of Mortis (S317)
The Citadel (S318)
Counterattack (S319)
Citadel Rescue (S320)
Padawan Lost (S321)
Wookiee Hunt (S322)
Water War (S401)
Gungan Attack (S402)
Prisoners (S403)
Shadow Warrior (S404)
Mercy Mission (S405)
Nomad Droids (S406)
Darkness on Umbara (S407)
The General (S408)
Plan of Dissent (S409)
Carnage of Krell (S410)
Kidnapped (S411)
Slaves of the Republic (S412)
Escape from Kadavo (S413)
A Friend in Need (S414)
Deception (S415)
Friends and Enemies (S416)
The Box (S417)
Crisis on Naboo (S418)
Massacre (S419)
Bounty (S420)
Brothers (S421)
Revenge (S422)
A War on Two Fronts (S502)
Front Runner (S503)
The Soft War (S504)
Tipping Points (S505)
The Gathering (S506)
A Test of Strength (S507)
Bound for Rescue (S508)
A Necessary Bond (S509)
Secret Weapons (S510)
A Sunny Day in the Void (S511)
Missing in Action (S512)
Point of No Return (S513)
Revival (S501)
Eminence (S514)
Shades of Reason (S515)
The Lawless (S516)
Sabotage (S517)
The Jedi Who Knew Too Much (S518)
To Catch a Jedi (S519)
The Wrong Jedi (S520)
The Unknown (S601)
Conspiracy (S602)
Fugitive (S603)
Orders (S604)
An Old Friend (S605)
The Rise of Clovis (S606)
Crisis at the Heart (S607)
The Disappeared Part I (S608)
The Disappeared Part II (S609)
The Lost One (S610)
Voices (S611)
Destiny (S612)
Sacrifice (S613)