For custom decals I used Solidesign for many of the different sets of milk car decals that I designed some years ago. I found Scott Wright of that company very good to work with in taking my B&W art and converting it to the colors I needed. He uses the ALPS process and the resulting product is thin and applies and hides well. Scott's ads are usually found in the small ad section in the back of MR. He is my choice for custom work. He also can work from photos.
Jim Abbott of Highball Graphics makes many modern sets and works in all scales. His O scale work is second to none. Jim also uses the ALPS process. Recently Highball has combined with Industrialmodels (Don Smith) to bring out a series of new O Scale decals that cover many of the latest schemes. I'm not at my desk as I write this, so I can't give a link, but you can Google the name and reach the site.
Regards, Ben Brown