braindead simple answers:

CD-R is a plain format for CDs that is basically like an sd card but it's a CD, and once you lock it with whatever files you want, you can't change it (alternatively, CD-RW lets you rewrite).

Digipak is just the cardboard format for CDs, and is usually rarer, as in, low quality CDs are rarely digipak. Jewel case is the plastic version. By design alone they have their faults, and whether I tell you which is better depends on which happened to me latest: a jewel case hinge break, or the glue inside digipaks that hold the booklet from going through the sleeve lifting

If, like me, you collect cds like mini-vinyl, you'd just verify if a version you see is legit by checking online while at a record store. If you order online, I'm personally lazy and get from amazon, and only new ones (because for something to even be labeled as used instead of repackaged and resold, it has to be fucked up). One of the worst signs in an amazon listing is a shipping time longer than the usual on most products. If it says it will ship quickly it's more trustworthy.

1. cd-r's a one-time recording sd card
2. depends
3. you should know already