Could audio line-out (from a PC) be used to flash an Atmel or PIC?
Actually I like your question, and I bet if one is allowed to use some simple external parts (like a diode for example) this might well be possible. Of course one might have to spend hundreds of hours to get a working prototype.

As others have indicated, if it is just for your personal use then you are much better off just spending a few bucks and buying a programmer.

If on the other hand you are looking to make a contribution to the open hardware movement a solution like this could potentially save thousands of people from having to buy a programmer. Possibly this would justify spending hundreds of hours of your time.