I sort alphabetically within each card type, with Academy cards separate for now. Same way most deck lists get sorted (in rule books, etc).
I also have them all in 9-card sheets in a binder, and with minor exception (Minor Heal comes to mind), all copies of a given card that aren't in books can fit in a single pouch in a sheet. That's for 2 first edition core sets, a Spell Tome 1, and 1 copy of each expansion (except Spell Tome 2).