This is my Cube list, a pool of cards used to play Limited Magic: The Gathering formats using an extremely high-powered Highlander virtual set (the Cube).
My list has several notable departures from the best-known, but rather than doing an exhaustive comparison, I'd rather talk about the underlying philosophy.
I want the various colors to actually accurately represent what the current color pie allows them to do: including stretches (Nicol Bolas, Planeswalker shouldn't be able to destroy enchantments) is fine, including flagrant violations is not (eg, Sylvan Library).
I want each of the stacks to have depth, allowing diverse archetypes, and to be reasonably balanced. I will not exclude cards on the basis of being imbalanced as long as they honor the color pie, unless they are also largely non-interactive. Creatures with Shroud (or Hexproof) are deliberately few in number simply because they tend not to add much depth to a game.
I strive for flavor-correctness in addition to mechanical correctness: iconic creature types and spell effects are preferred.
White themes: "go wide"/the group: token generation, anthem effects. equality: Wrath effects and exiling removal tied to a permanent (eg, Angel of Serenity, Banishing Light).
The collectivist aspect of White allows for a small amount of color bleed: Extort (Syndic of Tithes) is really a very Black ability, but when framed as a tax it makes thematic sense for White. Taxation also justifies the mana catch-up effects of Land Tax, Weathered Wayfarer and Knight of the White Orchid.
Blue themes: tempo: counterspells, bounce, card draw. puzzles/knowledge: cards involving player choice (eg, Master of Predicaments, Fact or Fiction, Gifts Ungiven)
Many of the card selections are intended to play up Blue's trickster nature: in particular, the Clone effects all have some subtlety that reveals their true nature.
Black themes: death: reanimator effects & creature removal. power: resource exchange, especially life-for-cards (eg, Dark Confidant, Yawgmoth's Bargain).
The fundamental difference between White's "equality" exchanges and Black's "power" exchanges is that Black is willing to make individual sacrifices.
Red themes: "go fast": burn, haste creatures. impulse: short-sighted exchange (Hammer of Purphoros, Through the Breach), chance (Gamble, exile-top-of-library as on Prophetic Flamespeaker)
Red has a significant token generation sub-theme that is intended to reflect its creative aspect. Unlike White, Red doesn't get straight-forward token generation: Mogg War Marshal has a drawback (echo), and Siege-Gang Commander really wants to just be a bunch of shocks, doesn't it?
Green themes: nature: creatures and mana are at the core of Magic and Green isn't willing to stray far from the core. growth: mana ramp, "evolution" (Survival of the Fittest, Chord of Calling)
Green is the least interactive color (in terms of spells) by design: it has a limited ability to put things "back to nature" (Naturalize, Bramblecrush & similar, Brooding Saurian), but no direct interaction with creatures.