Hidden Weapons
Many of these are pretty hard to find, but on most levels, there is a double weapon or a hidden weapon that will make your mission a lot easier.
In dataDyne: Investigation, if you get to this spot without being spotted, you can pick up a double CMP150.  I found it easier to just use a farsight and get all the guards from a distance. 
In dataDyne: Extraction, if you can get all of the first four guards without being detected, the last guard will have a DY357 Magnum.
Also in dataDyne: Extraction, if you can get all the way up stairs without being detected, you can go into Cassandra's office and pick up a grenade.
That grenade is used to blow a hole in the wall, and pick up a Dragon in the next hidden room. 
In Carrington Villa, if you can kill the sniper that is in this area on Perfect Agent in under about 40 seconds, you can pick up double CMP150s. 
Also in this level, on any difficulty, are boxes of ammo for your CMP150.
In Chicago: Stealth, if you use the barrels to blow up the big metal bin, you will find a briefcase containing a Bombspy.
Also in chicago, If you gain access to Pond Punk, you can pick up a second Falcon 2.  See the Pond Punk section under Mysteries for more information. 
In the G5 building, if you disarm all of the guard in the first room, one will drop a crossbow.
Killing this guy in the first Area 51 mission will get you double MagSec 4s.
If you blow up a little tank type thing, you can pick up a double falcon 2 silenced in the second Area 51 mission in the very beginning.
In the last Area 51 mission, if you turn around in the gas filled room, the scientists both carry Falcon 2s, so you can get double.
In Air Base: Espionage, you can get some proximity mines by going all the way to where the little rope trolley thing is.
Also in this mission, disarming the guard in dark clothes in this little security monitoring area will get you double DY357 Magnums.
In the Air Force One mission, if you disarm both of the guards in the first room, and take their key cards, you can use them to open up the closets and pick up double Cyclones.
In the Crash Site mission, if you disarm Trent Easton, you can pick up his DY357 LX Magnum, which can take out a guy in one shot!