If you intend to copy CDs to your new media, then MiniDisc is the way to go, without a doubt. With Type-R ATRAC (Sony), you'll get "CD-quality" recordings if your original source is of high quality.
I've made about 50 MD's worth of recordings via the headphone jack (using a 3.5 mm to 3.5mm plug) of my JVC mini-system, and they sound excellent. The newer MD units feature MDLP, which gives you a choice of longer recording times. For CD to MD, I'd use the SP mode, as that will preserve the original recording quality.
Some PCDP's have an optical out, which can be used with the MD recorder to make copies and maintain the track marks found on the CD. I have never done this, but many say the sound is superb.
Many will tell you that the LP2 mode of an MDLP unit yields good results. This is fine for mp3 stuff (which has lower bitrate performance than CDs), but I would not recommend it, unless, maybe, you wish to put a double CD recording on one blank MiniDisc.