stock wire works well
I did mine (E46) this past summer, and never posted my results - so here it is:
Used stock wiring with amplified components in each door. and the sound is amazing. i won't claim to be an audiophile, but I have a decent ear, and to me, the sound is brilliant.
even my gf noticed how clear and realistic it all sounded ... and she doesn't usually notice anything (related to the car).
I did have some RPM whine, but to correct that I simply rerouted the RCA cable from the deck so it avoided the (+) lead from the battery to the engine (along right side flood panel of the car).
Conclusions: stock wiring is fine (and colour coded in a logical way), I have a (corrected) .jpeg for the wire colour codes used in my car.