You start the game already in possession of a crate of trade goods. If you drop it off at New Zurich Orbital, in the Earth sector, you will receive 200 cr.
There's a second crate of trade goods in the Ganymede asteroid field (which is mentioned in TNS); it nets you 200 cr. from New Zurich.
During the first Kuiper mission (Security Breach), go to the Luna sector. There will be a freighter, the Ontario, which has a generator problem. Drop the Ontario's shields, or destroy the Shield generator to save their lives. They say you get paid, but I don't think you do.
In the scrap yards during the Hospital Emergency mission there is a crate of contraband towards the end of the asteroid field the frigate is drifting towards. Arman Patrioli gives you 850 cr. for it*.
Under the Star Patrol Farpost station is a crate containing Medical Supplies. It is only available to Bora, and it should be dropped off at Mercy Hospital for 550 cr. This is available during multiple missions.
In the Bora Gate Blueprints mission, there is a crate of spare parts on one of the landing pads in the Poranis Nebula. Drake facility, in the Industrial sector of the Hub gives you 550 cr. for it.
In the Scrap Yards while flying the Recoil mission there is a crate of 250 cr. near the station.
In the Nereus Research sector, there is a crate of food supplies. It's available in multiple missions.
Near Atlantic casino is a crate of 777 cr. (Is this a slot machine joke? 7-7-7?)
In the Illicit Pickup mission, if you're flying GalSpan, turn right immediately on entering Foothold, and fly past the station, you'll find a crate of Bora Mining Equipment in the asteroids. It's worth 650 cr, but I don't know who wants it. (I've been told that it is Apollo Research, but I've never seen them accept it myself.)
In Ceriphilon Production (GalSpan only) is a crate of spare parts in the middle "pathway" between the two big whatchamajiggers (drydocks?).
In the Color of the Nose mission (GalSpan) near the Arteris Array station is a crate containing 500 cr.
In the Draconis Ripstar Field: There is a crate containing 1000 credits towards the underside of the station in that sector.
In Redship Rory's lair, there are several crates: One contains contraband (Illegal Narcotic) and 5 crates each containing 100 cr. Arman Patrioli* in the frontier will give you 850 cr. for the contraband.
During the Risky Venture mission, there is a crate near the station with Medical Supplies. Mercy Hospital gives you 550 cr. For it.
While flying the Sour Colony mission there are two crates of food supplies on separate landing pads of one station in the Haven sector.
In the Twilight region, turn about 90� left as soon as you launch, and go about 10 KM. You will see the wreckage of a ship crashed into one of those blue domes. (Presumably, it's the Munn mentioned in the "Tachyon Manual" file.) Inside the ship is a crate of 5000 cr.
In the Demon Pirate lair, there is a crate very near to the station. It is Contraband (Illegal Chemical Compounds) and again, Arman Patrioli will give you 850 cr. for it*.
Sometimes Demon pirate fighters will be destroyed when you hit them with disruptor torpedoes. (This is more of a bug than a cheat...)
In Cassitor's station there is a crate containing Lost artworks, inside the station. Fly to the top half of the blue bubble-like thing, and you'll be able to beam it aboard. Malkar, in the Frontier region, will pay 1000 cr. for it. Available multiple missions, but you can only get it once.
In the Drone Abduction mission, there is also a crate of spare parts on one of the platforms in the Silicon Hive sector. 550 cr. from Drake in the Industrial sector for it.
In the Mercenary sector during the Identity Game mission, there are two crates. One contains lost artworks (1000 cr. from Baron Malkar) and the other is Illegal Chemical Compounds. (Arman Patrioli*, 850 cr.)
* NOTE RE ARMAN PATRIOLI: Arman is VERY RARELY available, but when he is, he's in the Dark Space sector of the Frontier region. I think it's random when he appears. The only mission where he can ALWAYS be found is the "Hunting the Hunter" mission (GalSpan), but that's useless to you, because you have to finish that mission before you can do the "Illicit Pickup" mission, and he won't buy anything until then. (There's only one crate of contraband up to this point anyways.)
This listing of hidden items is by no means complete. If you have found another one, please send it to me. Include what it is, where you found it, what mission you were flying. (Include your name and/or email, if you wish to be listed in the credits. If you do not include these in the BODY (text) of your email, I will assume you do not wish to be listed.)