To answer this question, consider how you'll be using the futon, but also what you want it to look like.
If you're going for a sleek, sophisticated look with a subtle frame, then you might want a thinner futon. Thinner futons are typically 4" or less thick and are even pliable -- which can add to their versatility.
If you're decorating a larger room and you have a substantial wood frame, a thicker futon may work better. Thicker futons may be as much as a foot thick, and resemble a traditional mattress more than anything else!