Not all of mine are configured the same, but close to 80% of them are set up this way at level 100 with Level 3 Garrisons:
Level 3 Mine & Garden - This is a no brainer since free ore, herbs, and food always come in helpful and they don't take up a small, medium, or large plot
Level 3 Fishing Shack - It's a free plot and I like fish so I take advantage of it
Level 3 Barracks - 5 more followers means I can assign followers to huts, mine, or garden and keep a body guard if I want and still have a good number of followers for missions.
Level 3 Lumber Mill - A good profile and a Timber plugin will load you up with wood in a short period of time for the mill to keep generating garrison resources(GR) for missions, the bunker/warmill, and follower rerolls if you choose.
Level 3 Trading Post - Fast easy way to produce additional GRs and I like having an auctioneer in my Garrison when I need it. The Reputation bonuses are nice to.
Level 3 Bunker/Warmill - Keeps the follower armor and weapon upgrades rolling in over time. I think it's worth it, but that's up to you. (Read below about swapping out the Bunker/Warmill for the Inn later on.)
Level 3 Storehouse - A must in my opinion for having bank access close by. Increasing the available work orders in the other buildings is a plus and the Transmog guys are handy if you need them.
Level 3 Tailoring Hut - 90% of my toons are max level tailors and the Hexweave work orders generate the free Hexweave Bags I use on my alts or to sell on the AH.
Level 3 Salvage Yard - Another good way to raise the item lvls of your followers and some decent BoEs here and there are always nice.
Level 1 Enchanter's Study - Basically just so I can DE BoP stuff for dust or crystals if my toon doesn't have enchanting.
*Once my followers have all reached item lvls that allow me to do the higher follower missions I get rid of the Bunker/Warmill and go with the Level 3 Inn so I can recruit followers and open up the Treasure Hunter missions with my followers.
As for missions, once I have most of my followers at 100 with an item level of 630-645 I focuse them on Treasure Hunting and Scavenger Missions to increase gold and GR income. It's also good to keep a team set up that can 100% handle any mission in the game.
Here's a really good guide to Follower setups for anyone interested:
Garrison Follower Setup Guide