Most important thing is running them so the curves are smooth and making sure the cut ends are straight and clean. The trick is walking the line between not being too tight, but not so loose that they flap around while riding I like to form them something close to the curve they'll take when installed and cut them like that. With shift cable, if you just get your measurement and cut the housing when it's straight, when you curve it for installation, the metal wires inside the housing will take on an unwanted angle at the end with the inside of the curve sticking out farther than the outside because the arcs they scribe will be different lengths. If that's not an easy thing with the tools available, you can cut the housing when it's straight then form it into the curve you want and grind the end so that it's at 90 degrees with a bench grinder, belt sander, etc. Brake cable is less fussy—just make sure the metal coils within the housing don't drag on the brake cable and that the inner plastic jacket is fully opened (I cut my housing with an angle grinder, so it melts the inner liner at the area of the cut, but an awl or round jeweler's file fixes that easily).
I've not really had an issue with plastic ferrules, but they can bend at the cable stops if they're at the end of a section of housing that moves a lot. I've only really had this happen at the rear derailleur, but it didn't seem to cause a problem. I would use some kind of ferrule, though, as shifter housing is made up of parallel cables running the length of the jacket, so at the ends, they're liable to float around if they don't have something stopping them. In theory, the cable stops can accomplish this, but they're usually designed to be used with ferrules, so they'll allow way too much play and opportunity for the wires to move around inside the jacket and possibly cause it to split.
Another thing I do if the cable stops are located in a way that allows it, is cross the shifter housing past the head tube instead of using the cable stops on the same side as their shifter. It will mean that the cables will cross over each other under the down tube in an X pattern to reach the proper channels in the cable guide under the bottom bracket, but the drag from that is slim to none. The benefit is that the housings take a cleaner sweep into their cable stops both looking better and reducing friction while also flopping less when riding.
