It seems to me there are a few of ways to deal with this problem, but I'm not totally happy with any approach.
1) List IE6 development as a separate line item, with a cost beside it that the client can opt to go for or not. The problem with this is they could take that estimate to another company who might say "well our websites work in EVERY browser, no extra charge", whether or not that's actually true.
2) Tell clients up front that if they want a website that uses cutting-edge front end technologies, they'll have to live without IE6 support. Offer to install an upgrade banner/alert for no extra charge. A lot of clients don't understand that IE6 is turning 9 next year, or they don't understand that using a 9 year old browser is like driving a 25 year old car.
3) Continue along the same path of just making sure everything works in IE6, even though it slows down development, adds to costs, limits the design and programming departments, and contributes to developer alcoholism and severe workplace swearing.
This problem has to be cropping up at every design/development studio that builds websites using the newest technologies. How do the rest of you deal with it?