It essentially means that something is the same thing. The two things you're talking about are really similar.
Tom: "Hey we can either rent a Ford Taurus, or a Mercury Sable."
Eric: "well 6 of 1, half dozen of another."
used when someone asks you to do something you don't have time to do. typically used when you are in the middle of planning a large project, or are otherwise really busy.
1st guy: "can you pick up a sanwich for me?"
2nd guy: "not today dude! I've got shit to do!"