My cards are probably a little too meticulously sorted, first by set and then by collector number (which equates to sorting each set by colour, and then each colour alphabetically). I do this because when I'm looking through my boxes, I'm usually not just browsing. I'm looking for a specific card, and this system makes it as easy as possible to find.
I think your friend's logic is a bit flawed; not every deck "needs a few uncommons and a rare or two." Equating rarity to quality presumes that WoTC always makes all rare cards better than all common cards, and that's just not true. Lots of hugely powerful cards use many commons, and I've seen a lot of decks that are filled with rares and are still useless.
There are probably a million or so articles on deckbuilding that I won't bother re-hashing, but I will break down why why I think my sorting system is the best. When I build a deck, I:
- Find a deck archetype online that sounds interesting, or find a card that seems fun and/or powerful. For example, I see Mindcrank in the NPH spoiler list, see that it combos well with Bloodchief Ascension, and try to make a combo deck out of them.
- Scour forums and blogs for people who have had the same idea, and figure out what would be needed in such a deck. To make this combo work, I need to do a few things: find both parts of the combo, get them into play and protect them, get counters on the Ascension either through burn or proliferate, set off the combo through discard or burn, and I have to protect myself until the combo is set up.
- Given that information, I start to put together an initial decklist using Gatherer. Because the combo uses black anyways, I look up black cards that provide the abilities I need (e.g. Duress, Despise, Inquisition of Kozilek, Sign in Blood, Dark Tutelage), and since I likely need both card draw and burn with proliferate as a bonus, I start to splash red (Volt Charge, Staggershock, Ember Hauler) and blue (Tezzeret's Gambit, Mana Leak). I pick 9 cards to run 4x each of, figure out my mana base with basic lands, and I have a first list.
- NOW, I go to my box and get the cards that I'm going to use out. I whip up some proxies for anything I don't have, head off to the local shop or MTG Online, and playtest until my eyes fall out. Every game, I take notes of what worked and what didn't. Any time I had a card sit unplayed in my hand, that's may be a sign that it should be replaced with a different card that fills a need you didn't have before. Maybe I'll decide that I'm drawing cards fast enough from Dark Tutelage that I don't need blue after all, and I replace those cards with more burn because I didn't get enough. As you play the deck more and more, you refine it further and further until you're happy with it. Then, and only then, I go out and trade/buy the cards I'm missing.
- If you want, you then figure out what kind of decks you're likely to play against (the metagame), figure out how those decks might throw a wrench into yours, and build a sideboard to throw a wrench into theirs first.