Like what, buying some uncleaned ancients and removing dirt or just storing cleaned? If already cleaned/what you own already, 2x2 flips are my preferred method and then storing them in a binder with binder pages. People like Doug use Trays but small space keeps me from using that method.
One specific example, I handled one copper to the point that the high points are starting to shine. Is this desirable? Should I care as long as I am enjoying myself?
I wouldnt constantly handle them like change in your pockets. Even though they are already cleaned and can be handled like common change, constant handling will of course bring more wear. I still hold mine by the edges most the time.
Shininess will certainly detract the value, but if it's a cheap Constantine or something, I wouldn't worry about it as long as you're enjoying yourself. And it can be fun to keep something like that in your pocket just to bust out on people like it's no big deal. It totally isn't, but most people don't know that. As for long term stuff, you probably shouldn't handle things that much, though you obviously don't need the care that's expected for modern coins. If you're using flips, try to use PVC free ones, and if you're able, keep your bronzes in a dry place. Moisture can trigger bronze disease, and that's a big pain in the ass.
Always hold coins by the edges so you avoid touching the obv and rev faces of the coin. But if it's a cheap coin, touch and rub away to get that ancients thrill. And as posted by Gao use PVC flips or other such archival storage materials.
I find them too shallow for my liking, and too small - I would like to keep any pedigree tickets WITH the coin. I'm still working on devising my own system. More to come!
Tickets from previous owners or auctions. Here's one from 1895 in my collection: http://www.forumancientcoins.com/gallery/displayimage.php?pos=-54093