Zvi wrote an extensive article on this very subject matter, look it up in the columns archive section under Zvi. Any way, this is how I do it:
From scratch, I think about how I would like to win a game i.e. through board control, weenie rush, lock-down (I once played a 'Bastille a la Prison deck that had absolutly NO kill cards in it, just stuff like Winter Orb, Gerrard's Wisdom, Gaea's Blessing, Armageddon, Propaganda, Wrath of God, a few Gratuitous Counterspells, mana rocks, etc...) It's good to have the end goal in mind.
I then decied if I want this to be tourney viable or just a "Fun" deck to mess with.
Then, I do a little research to see if I can find a similar deck or concept elsewhere or I post a deck list and have folks look at it.
I do have some templates I work with for deck archetypes I've built before:
Stompy:
Mana Curve 16x1cc / 12x2cc / 8x3cc / 4x4cc / 1 Hurricane. 16 land. The creatures have to give as much bang for the buck and is allowed to have a drawback like Rogue Elephant.
Control Deck with Blue: 24 lands. 16x counterspells like in T2: 4x Counterspell, 4x Rewind, 4x Miscalculation, 2x Power Sink, 1x Thwart, 1x Misdirection, 4 Brainstorms and 2x Morphlings. If I'm using another color splashed in I focus on that color's strength and go for it, like Red; I'll add four Seal of Fire, 4x Lunge and 2x Hammer of Bogardens. If Black; I'll add 4x Terror, 4x Massacare, and two Engineered Plague. If White, I'll add 4x Wrath of God, 4x Disenchant or Seal of Cleansing, and two Story Circles. If green, well I just use my standard ConTroll deck.