Yes, I'm of the opinion that every coin is a custom shot unless they're modern; ie., a series of Morgan dollars. However, a basic setup can still work with just a bit of finetuning needed for each new coin.
Ancient coins that are worn smooth and are shiny all over give me nightmares... some coins defy a good photograph, that's for sure!
I'm only familiar with Photoshop but it's hard to recommend it for everyone because it's so expensive. Scanners and digital cameras come with bundled software that should be good enough (I think).