Turrets
No one ever expects a beacon on a turret, that is simple.

Hand of Nod
Right under the MCT. No one ever finds it, because they only look on the pedestal...

Barracks
I always put it between the two doors on the inside, no one ever sees it.

War Factory
In the corner of the garage where the vehicles come out, or on the control panel thing, in front of the window... you know the place...

Airstrip
In the circle thing in the building( cant beleive no one looks there)

Power plant
On that control desk thing in the middle, facing the MCT.

Refineries
Once I successfully made it while the harvester docking, I put the beacon in that docking garage thingy, and no one found it...

Obelisk/AGT
Haven't found fail-proof way yet...