Yes, I have with the inspiration of an article by Fred Dole in one of the train magazines. And yes, the hardest thing to do is to get a match of the color on your computer with the paint color of the train car. It takes some patience and a lot of tinkering.
Black is obviously the easiest to match and my first project was making a Procor tank car from a Lionel 3-dome traditionally sized model. The decals simply do not exist for making such a car, so I tried the paper technique and am real happy with the way it came out. This car worked well because of the placement of the rivets in the car, I was able to make 2 rectangular areas where the lettering would be and to glue those to the spaces on the tank car, so that no visable edges of the paper show at all.
I've also done a Norfolk Southern engine. Here there are decals, but getting the correct size from the decals was another issue, so I did it myself. Here's a case where upon close inspection, you will notice the areas of which the hearld and lettering are. But again, with a black locomotive, it is really only evident upon close inspection. You certainly would never notice it watching the train working on the layout.
I've done a couple of CP Rail box cars out of the K-Line 5000-series cars (the former Marx type). I mixed decals with the black/white hearld which I made on the computer to get the size precisely right.
Stepping up another level, I did a Conrail unit in this method and after a good deal of tinkering, managed to get the color on the paper nearly perfect. Enough so to make me happy and encourage me to try some more projects like this.
This works fine for me, being an 027 operator, because I am not a rivet counter. Whether such results would please a true prototypical scale operators is another matter.
I prefer to use decals, and like Microscale the very best. But it is getting SO MUCH harder to find decals now because they do not sell enough in O scale, so they are not being made (SO forget it all you folks who hope for unpainted cars from the train makers... it's not gonna happen, not when thye biggest decal maker is dropping O scale decals in droves).
Luckily, because I am a semi-scale 027 operator, I've been able to cob HO decals meant for larger cars or engines and use those on the smaller kinds of 3-rail trains I run. Still, there are gaps in this between what I want to repaint and what I can find decals for. Hence my desire to begin experimenting with making paper sides for some cars and engines.