I'm trying to count all my cards, but it is not always worth it I believe.
I do have a quite simple system.
Because I also collect them, I have all cards at least once in a binder, organized in the same way Wizards does it (For the sets before Exodus, after that you can sort on card number)
I put the cards in a card box of 4 rows, in the same order as the binder.
Sorting goes quite fast, you don't have to switch a lot of cards when you add a new pile into it and so on.
Also you can sort them visually, you see every card in the binder.
The rares are also among those because the boxes preserve the cards very well.
I do however not sort the basic lands.
They are kept in a seperate box, except for special lands, they aren't in the binder
Little note: There are several Commons and uncommons that are worth something.
I think of Duress, Ostracize, Goblin Lackey, Rancor, Mana Leak...