As Mister B notes, many of these cars' trucks can be re-used by simply cutting off the coupler boxes. It's then often very simple to add Kadee couplers mounted in their own draft gear boxes - #5s work well on most freight cars, although they may need to be shimmed down (use sheet styrene of suitable thickness). You should get a Kadee height gauge, and probably some Kadee fibre washers, too. The latter are for cars that sit too low, and are placed between the truck and the car's mounting bolster. You can glue the coupler boxes in place, but it's advisable to screw mount them if possible, so you'll need a pin vise, a #50 drill bit, and a 2-56 tap.
If you want to change the trucks to screw-mounted ones, usually the hole in the car's floor first needs to be plugged. Use a suitably-sized piece of plastic sprue or styrene rod from Evergreen. The material for the plug should be .004"-.006" larger in diameter than the hole being plugged. Coat the inside of the hole and the outside of the plug with solvent-type cement - I use lacquer thinner - wait a few seconds, then force the plug into place. After the cement has hardened, shave-off any protruding part of the plug, then drill and tap as you did with the couplers.
If you want to replace the trucks themselves, there are many after-market ones available. You can also buy plastic sideframes in several styles (with or without the plastic wheelsets) from Accurail.
Here are a couple of upgraded cheaper freight cars.
This one is from Varney, but the same car was also offered by LifeLike, in both open and covered configurations:
A Tyco four bay hopper (available from several manufacturers, I think) I shortened mine to three bays, but the truck and coupler conversion work is the same as outlined:
I'm not sure who made this one - I picked up a couple of these, bodies only, for a buck each. This one has a Train Miniature floor, but a simple floor can be made from styrene:
This gondola is from Con-Cor, but was also offered by Revell. I lowered the ride height by removing the car's underframe, then added bolsters built-up from sheet styrene.
It can also be modified into a fairly accurate rendition of a Pennsy G-31:
Here's the modified underside (due to the thin floor, the couplers are cemented in place):
This flat car is from LIfeLike, I think, but others may have offered it as well. I removed the original plastic deck and floor, making a new, flush-top floor from .060" styrene, then added a new deck built-up from 3"x8" scale stripwood. The bulkhead ends are from a Walthers GSC flatcar.
I did retain the original underframe, but filed-down the bolsters in order to allow the car to ride lower. This necessitated removing part of the underfloor, to allow clearance for the wheel flanges:
I made an identical car from an almost identical Athearn flatcar, using mostly the same methods, but discarded the separate underframe completely. Truck-mounting bolsters were built-up using .060" sheet styrene:
Here's a look at one of the wood decks, an easy-to-add detail for many open cars. The boards are secured to the plastic sub-floor with contact cement:
This is a LIfeLike (Proto-no-thousand) 36' reefer. I change the trucks and added Kadees, as outline above, then added a few details and some paint and lettering. One of these days, I'll get around to making a new roof (the roof is a separate piece) as ice service reefers often had their bunkers and hatches removed.
Another reefer, this one from Tyco. Trucks and couplers, plus a few details. Lettering is from C-D-S:
These doubledeck stock cars are from Rivarossi. I removed the moulded-on floor moving mechanisms, then narrowed the cars by sawing them in half lengthwise using a carpenter's handsaw. After cementing them back together with lacquer thinner, I added a few details, plus paint and lettering:
I also re-used most of the original underframes and the trucks, but cut-away most of the floor and replaced it with .060" sheet styrene. This got rid of the unprototypical moulded-in-place brake gear, so I added "K" brakes from Tichy, along with some wire rigging:
What you wish to get from your "free" cars will depend mostly on how much you're willing to invest in them in time, although there'll likely be some money required, too. If you enjoy modelling, they can keep you busy for a long time.