If buying any quantity from the same seller, $1 with separate shipping is always the better choice since most sellers give a big combined shipping discount. Say you bought 10 cards. In my choice it would be $10 plus maybe $3.50 for shipping. In the "free" example, it would cost $20.
There is a relatively new real-life example of this concept to try for yourself. Burbank just relisted all of their base commons at $1.69 with free shipping in eBay and raised the price of most other cards slightly. Find several cards you want and compare the total cost against online sellers like Cards & Games, Triple Play, etc. that have similar inventory. See what the difference in cost will be.
Cards listed in my collection are not for sale or trade