There are 17 missions in total, becoming available as you proceed through the story. Don't be too concerned if you miss any, because as The Kudi Zone points out, "all missions become available at the end of the game after the credits."
(There may be some mild spoilers ahead, you have been warned)
Sidenote: If you feel I've missed something, please leave a comment below so I can correct the solution.
- Dinki-Di: Retrieve Chums buggy and Dink-Di from Chum's Hideout and return both to Jeets Stronghold. Very easy unless you get ambushed on the way back.
- Lust for Powder: Free Blas Cap from the slavers in Thrall's Cave. Easy as any other camp attack.
- Ashes to Ashes: Locate and mark the two saltpeter sources and the sulfuric vent. Very easy task in and of itself but you will need to drive a fair way into Gutgashes territory so be prepared for a load of harder opposition on the roads.
- Playing with Fire: Two stage mission. First, hijack a fuel truck from a convoy and return it to the stronghold. Second, drive the now explosive-rigged truck to the barrier wall to the North and detonate.
*Highly recommended doing all of these ASAP as it will make your life in the wasteland so much easier*
- Ironclad Faith: Recover a subway car from the Buzzards and mark it's location with a flare once it's out of the tunnel. Pretty simple as long as you take it slow and avoid the traps the Buzzard leave around.
- A Sign of the Gods: Enter the storm drain between Gutgashes and Pink Eyes territory and recover a religious symbol (anchor). Easy but you'll need to travel through Pink Eye's turf so expect to see some serious opposition.
- Beat to Quarters: Defend the stronghold from convoy attacks. There's only three of them and taking out the main vehicle is enough.
Pink Eyes Stronghold
- In Due Time: Take down the Tyrant's Lash top dog camp and recover the attached water collecting sail. One of the harder camps in the game so prepare for a tough fight.
- Our Daily Bread: Find a buried church in The Dunes. Much off-road driving involved but the rest of the mission is fairly easy.
- Exodus: Transport the duneship to it's launching point. Can be quite a difficult mission as you have a long way to go through hostile country and only your shotgun to defend yourself. The truck itself is also quite a handful to drive.
Deep Friahs Stronghold
- Where There is Smoke: Enter Gastown Underbelly and close four gas valves. Be warned that while the gas is flowing, you will constantly be losing health so make sure your health is as maxed as possible and your canteen is full before you start.
- Torch Them All: Locate the Arkytekt's camp and take it down. This must be started at night.
- A Shot in the Dark: Mission given by Hope. Find the hidden hatch in The Dunes and locate the lift kit. Piece of cake.
- In the Buzzards Belly: Mission given by Hope. Search the North Tunnel for the abandoned War Rig and recover the sniper magazine upgrade.
- As the Wrench Turns: Mission given by Chumbucket. Locate Chum's stash in the Underbelly.
- Ghosts of Our Past: Mission given by Hope. Locate the Tomb of the Rider and return the vehicle to the nearest stronghold (Gutgash).
- Razzle Dazzle: Mission given by The Outcrier. Steal Crow Dazzles speaker truck and return it to Gastown. The speakers will be attracting all manner of hostiles on your journey and you'll have nothing but your shotgun to defend yourself. Insanely difficult if you get ambushed by Stank Gum boys on your way through Gastown.