Hi Dan, welcome to eGullet and the wonderful world of confectionery.
There is a thread about packaging somewhere with links to sources. A lot of it is personal choice on how you want things to look, how much you want to spend, whether you want to fold boxes or use set-up, how much plastic you're comfortable with, etc. Plenty of us can commiserate that packaging takes at least as much time and effort as making the product 
but here's my take:
2 hours ago, Dan K said:1. I want to get some hemisphere molds, but I just can't decide what size to go with. I'd like to dabble in making cream filled spheres, but I also want to make some that are just hemispheres. Does anyone have specific dimensions for these that you think customers like?
Seriously consider pre-made truffle shells for the full spheres. There is a magnetic sphere dome out there that a few of us have tried and hated. I find perfect hemisphere molds can be tricky - if the shells release from the mold before you are done filling and capping, they can slide out and lead to messy edges when filling spills over into the mold. This has been happening with some of my Easter eggs and is annoying. I'm mostly using the CW 2295 dome these days.
Quote2. I'm also interested in trying some basic mold decorating, mostly just to differentiate flavors. One easy way seems to be colored cocoa butter drizzled in before adding the shell. I get a little overwhelmed with the choices online. Is this a reasonable method? And if so, do you have a specific product you use?
I like Roxy & Rich cocoa butter colors though Chef Rubber are good too. Consider luster dust and piping a contrasting chocolate as other easy decor.
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3. For the truffles and creams, I've been putting them in little mini baking cups, and then packaging in a box. But I've also seen them just put loosely into the box without the extra cups. Does anyone feel strongly about this?
Cupping is annoying but I'd use a cup OR a well-fitting tray. Right now I have boxes with trays for bonbon assortments, though I use cups and different boxes for bulk orders to certain customers, and I have one box that is such a snug fit that I use nothing because they can't slide or rattle around at all.
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4. Another packing question - I like to sprinkle the hand-rolled and dipped truffles with decorations that can be a little delicate (i.e. chocolate curls). Obviously, this is fine if you're putting them in a box and handing the box to your friends. When you're selling at a market, that box might be put in a bag and jostled around. Is this still safe to do? Or should I skip that kind of decoration?
Definitely be concerned. Box a few up and shake then around several times, turn them upside down, etc.
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5. More packaging question - for the candied nuts, orange peels, and turtles I've been using cellophane bags and twist ties. This doesn't seem appropriate for selling. Any suggestions for packaging items like these?
Nothing wrong with that. Consider heat-sealing the bags for freshness and to tamper-proof. Find a more special twist tie - metallic or patterned or with a bow attached and a cute sticker and you're fine.