We use a small surface mount connector that has two alignment pins to ensure proper alignment. It works fairly well. I'm thinking that this simple alignment solution might work well with lead less parts like a BGA or QFN. I can hand assemble QFNs fairly well but getting proper alignment can be a challenge. A couple of alignment pins on the part and a couple of alignment holes in the PCB cell would make alignment easier.
(http://www.smtnet.com/Forums/Index.cfm?CFApp=1&Message_ID=66232)