I saw something posted on quotes a while back, but have not seen any updates or even is this is being considered as a possible enhancement. It would be great if an estimate could be created just as an invoice (but marked as an Estimate/Quote) is now with the ability to specify a deposit amount such that when selected, and paid, the estimate would either convert to an invoice automatically or allow an Admin to convert an estimate to an invoice but still allow payment against the estimate. When converted the Invoice would show the full amount of the Invoice less the deposit amount and date of deposit and the balance due.
Since an accepted estimate may have a future due date for the balance due, the Admin would need to be able to adjust the due date of the newly updated Invoice.
In a perfect world the estimate would allow for a "good until" date where if not accepted (money paid against it) it would be removed from the list.
And, of course, if you build this then people will be asking for scheduled payments against an invoice to allow for milestone completion payments, but for starters what I described would be sufficient for many people.