It will be nice to see an S-2 in something other than CDF markings.
There are a few options for custom decals depending on what you need. One of the easiest is just using microsoft word. You can use it for the lettering and by inserting cropped and edited photos of markings you can use it to scale logos and such. The Word art feature lets you make more fanciful lettering as well.
Microsoft paint can be used to make up logos fro scratch, then again inserting the finished design into word to adjust the final size.
That is the easy & cheap method since it uses a program most people already have. The downside it they are pixel based images so adjusting the size tends to distort the image and the detail is a little fuzzy on smaller images.
Testors offers a decal making program, but from what I've seen of the free sample and heard from people who bought the full program, it doesn't really offer much over the method I described above.
If you expect to get serious about custom decals, vector based programs like Corel Draw work well. The images in a vector based program do not use pixels so there is no distortion when altering size, so you can make a nice big image, say 6x6" making it easy to draw in fine details, then shrink it down to 1/4 x 1/4" for your decal. You may lose some detail just because you can no longer see it, but it will be there at least down to the level of precision of your printer. These programs are not cheap, but sometimes you can get a student / teacher version which is far more reasonable in price. Another option would be to use the program somewhere else (library or college maybe?) then save the file as a pdf so you can print it elsewhere without needing the program. Sometime you can download a 30 day trial of a program which would work for a one time need (or work like crazy in that 30 days and make up a ton of decals )
The other issue is your printer, standard color inkjet and laser printers work fine for many decals, but don't do white or metallics, light colors (grey, yellow etc) can also be a problem on a dark colored model.
There are several brands of decal film, Micromark, Bare Metal Foil and Testors are ones I've used, but there are many others. They are available in clear and white film, and you need to buy them for your type of printer. You can not use inkjet film in a laser printer or the reverse.
The easiest option is just go with a custom decal maker. There are several out there, I sent some designs to diecast & decals earlier this year and they came back very nice. He uses an ALPS printer so white & metallics are possible. You could check with Joe Osborn at Fireball Modelworks too, I think he does some custom printing in addition to his regular line.
I know diecast and decals will also do design work in addition to printing if you send a photo of the decals you need. I did my own art work but he was very helpful giving me some instruction to tweak my designs for the best effect. Using a custom printer for you decals costs more than doing it yourself but compares to other aftermarket decals so is pretty reasonable.
http://diecastanddecals.com/
http://webpages.charter.net/osborn82/index.htm