How to choose paint colors?

I stopped by Home Depot tonight to pick up some paint swatches. I am finally ready to start thinking about painting some walls in our house. How on earth do you choose paint colors though? Jeesh. Austin and I don't exactly have a great eye for decorating, or picking things that match. In our townhouse, we had a deep dark purple living room, a bright yellow dining room, and a red red kitchen. We loved it, but man it just did not flow and it sure was...not subtle in the slightest. So I would prefer to actually pick colors that will flow with each other since our rooms connect.