Which missions can I earn the Ghost and/or Smooth Operator bonus on?

Solution 1:

Credit to Darth Bieber on Trueachievement.com. (Gh) = Ghost, (SO) = Smooth Operator.

Sarif Manufacturing Plant (Milwaukee junction):

1. Entering the plant (Gh)
2. Reaching the server room with the Typhoon (Gh)
3. After having dealt with Zeke (Gh)

Detroit 1:

1. Retrieve the Dead Terrorist's Neural Hub (will sometimes work by convincing Wayne Haas to let you in. If you don't and need to infiltrate I suggest going by the sewers it is much easier than the other two access points) (Gh)
2. Locate and shut down the antennae in Derelict Row (Gh)

FEMA Camp:

1. Infiltrate the mercenary compound (Gh) (SO)
2. Locate the mercenary leader (Gh) (SO)

Hengsha 1

1. Investigate the Penthouse Apartment (Gh)
2. Find and speak with Tong Si Hung (Gh)
3. Escape the Alice Gardens Pods ambush (Gh)

Tai Yong Medical

1. Enter TYM's tower by passing through the Pangu (Gh) (SO)
2. Find and view Van Bruggen's recording (Gh) (SO)
3. Confront Zhao in the Penthouse (Gh) (SO)
4. Escape and get to the hangar (Gh) (SO)
5. Open the hangar door (Gh) (SO)

Picus

1. Escape the ambush by reaching a lower floor (Gh) (SO)
2. Get to the funicular (Gh) (SO)
3. Summon the funicular (Gh) (SO)
4. Get inside room 802-11 (Gh) (SO)

Detroit 2

1. Go to the convention center and obtain Sandoval's location from Taggert (can be done through conversation or sneaking into his backstage room) (Gh) (SO)
2. Find and confront Sandoval (Gh) (SO)

Hengsha 2

1. Escape the construction site (Gh) (If you are trying to save Faridah Malik then by all means go right on ahead. It will not affect Foxiest in anyway shape or form. However, if you do decide to take out the soldiers [non-lethally or otherwise], then you cannot get Ghost as someone will see the robot exploding)
2. Find Vasili Sevchenko's GPL device (No ghost nor smooth operator)
3. Rescue Tong's Son (This is a pre-order DLC from Gamestop. If you have it you can get ghost and smooth operator. If you don't have it, it obviously doesn't affect you.)
4. Meet Tong in the Harvester Hideout (No ghost or smooth operator)

Seaport

1. Retrieve Tong's package from the shed (Gh) (SO)
2. Place the C4 on the administrator's desk (Gh) (SO) (you will not see these bonuses pop up because it cuts straight to a cutscene. If you're unsure, the way to confirm that the bonuses were awarded is to make a note of your XP before you place the explosive. After the cut-scene ends, you should be 1000XP better off. 500 (Gh) + 250 (SO) + 250 (Getting Things Done))

Omega Ranch

1. Disable the signal jammer (the only way I found to get this smooth operator bonus was to do it in the first building you see once you leave the storage shed you wake up in. If you try and disable it from the tower you will most likely not get it. I didn't receive it the two times I tried on the tower, but I got it the first time I disabled it in the building. This will enable this SO and the search for signs of Megan's team). (Gh) (SO)
2. Search for signs of Megan's team (Gh) (SO) (see above)
3. Find and speak with Nia Colvin (no ghost and no SO)
4. Find and speak with Eric Koss (no Gh and no SO)
5. Find and speak with Declan Faherty (no Gh and no SO)
6. Upload the virus to the security computer and enter the restricted area (Gh) (SO)
7. Use the Leo Shuttle to reach Panchea (Whether you save Malik or not there is no bonuses here so feel free do handle this section as you like)

Panchea

1. Get inside the tower and disengage the lockdown (Gh) (SO)
2. Reach the broadcast center (Gh) (SO)

Solution 2:

I don't think anyone has a specific list, but to speculate:

• I suspect both are only tied only to "main" missions. Programming-wise, the game is probably keeping flag(s) for whether you "failed" somehow (being seen, triggering an alarm, etc) while in a certain geographic area and having a corresponding "active mission" going on. If you reach the next mission-phase without the flags being set, then you get the reward.

• Smooth Operator can only be achieved in places where there is an alarm-system of some sort which can be triggered. If there is no alarm system, you simply can't get it, no matter how stealthy you are. If I recall correctly, Alice Court Gardens are one example.

On a side note, I wouldn't worry too much about maximizing XP. Almost nobody has a playstyle that varies so much that all of the augmentations become useful.