Thanks for the suggestions. It is a bit late now though, as I have almost finished the quote feature. Creating a quote based on an invoice seems a bit back-to-front - nBill 2 will allow invoices to be generated based on a quote though!
Quotes can be emailed, and correspondence about a quote can be recorded on the quote record (eg. if you have to ask the client for more information). There are no specific discount features, but offering a discount if the quote is accepted within a certain time frame is a good idea. That will not be in the first release though.
You can include 'small print' on a quote, which could include terminology such as 'by accepting this quote you are agreeing to xyz', but I have not (yet) added the facility to enforce acceptance of terms. I am currently working on payment processing.