I don't know of any programs specifically made to design pool cues. Maybe they're out there somewhere. You could use just about any drawing software program (CorelDraw, Illustrator, etc.). Designing a pool cue is like any other drawing. It all depends what you like, what shapes you want, how complex or simple you want it to be, etc.
However, I think you really mean to ask about the programs that cuemakers use to create their designs and generate the CNC programs used to cut out the inlays and inlay pockets. Most cuemakers use some type of CAD program.
CAD programs are extremely powerful programs and can be very expensive. Thankfully, since all we cuemakers really need to know about CAD/CAM is pocketing (making the inlay hole) and profiling (making the inlay piece), the learning curve isn't horribly bad. Of course, there's more to it than that, but that's a good place to start.
Like a lot of cuemakers, I use BobCAD. It's quite easy to learn, and training DVD's are available.