Jewel cases, because they can always be replaced (I once had a digipak with most of the "teeth" missing on the, uh, CD-holder part, so I was pretty much fucked), and the digipak has some occasional annoyances: Deathspell's latest has no booklet-holder, Asunder's latest includes the disc in a hidden envelope, and neither of my Paysage d'Hiver CDs can fit on the same shelf as the rest of the "P" bands in my collection...they're instead forced to the top shelf, just in front of the "A" bands, which nicely blocks the obnoxious "Xtreem Cult" insignia on the back of my Abhorer CD, but then I have to worry about observers assuming an unwarranted importance for the extra tall CDs on the top shelf. I CAN HARDLY STAND IT!!!!1
edit: It looks like most of my points were already covered.