In the early game, I tend to choose colonies based on their potential resource production. If a non-breathable can produce more of a resource that I need, it gets colonized before breathables that are poor in that resource. Colonizable worlds with ruins are a priority regardless of atmosphere or production capacity.
Later on, when I've met other races, I'll start colonizing marginal worlds just to keep others from claiming them.
[Edit] You're not supposed to edit the question while I'm typing a reply.
I typically don't start building population shuttles until I've run out of good candidates for colonization.
Production bonuses from population are based on fixed numbers, not percentages. If your homeworld maxes out at a boundary, production will drop every time you move pop off it.
The values of the boundaries are listed in Settings.txt, and the current effective bonus is listed on the planet's Abilities tab.
[ August 18, 2002, 18:58: Message edited by: capnq ]