IMHO it really depends on the project and the aim of it. If you are producing a consumer application for example - most users on Personal PC's have strayed away from IE6 as part of Windows/Mac Upgrades to either at least IE7 (if not IE8) and Safari 3 (now 4). Of course, FF has huge market share and the up and coming Chrome etc crowd.
The problem is - if you application is broadly audience - such as a news site - most enterprise legacy applications still run on IE6 and require it - inferring that the corporate/enterprise IT crowd will still run IE6.
The best way maybe to structure your site (if you really want to use CSS3) is to idealistically build it entirely in CSS 3 - and have a separate style sheet for IE6 elements if you are getting a lot of traffic from IE6 (use JS to detect browser). Then, you can always toss away the IE6 when its no longer needed without having to recode the entire site.
Alternatively, stick to CCS 2 if you feel your traffic is going to incorporate IE6. I don't see, personally, the point for restricting your application - its tough enough to promote a web app so I dont see why you would want to make it tougher by reducing a (still large) % of the browser market.
P.S - Either way you go, pop a "best viewed in Chrome etc" on your site - always helps :D