Rares, Chests, Etc
I have been using a combination of rVignette and HandyNotes_DreanorTreasures (HNDT) to get lots of loot. As you run around rVignette will pop up a message when a rare is nearby. HNDT marks all of the rare mobs, chests and other lootable items on your map. Rare mobs are marked with a skull. Check the skulls on the map for the name rVignette popped up and head toward it. The icons HNDT puts on the map will show you what loot can be gained at that location when you hover over them. Loot ranges from gear to garrison resources and vendor trash.
Master Plan will put the missions your followers can complete most successfully on the top of the mission list. It will highlight the follower skills required for each mission. One of the best features is completing all missions on one screen which then shows the loot you received. No more animations for each mission! It also has a feature that shows you the teams you can send on missions and their success percentages, click the team you want and it automatically puts the followers in for you.
Broker Garrison - is an LDB addon that shows the status of missions, shipments and buildings. It also allows you to modify the way WOW alerts you for these items.
If you are looking for a guide on Garrisons Wowhead has a nice one.