Nintendo has created a product page for Mega Man 6's Nintendo 3DS Virtual Console release. It's listed to launch on the eShop this Thursday, June 20th for $3.99 US. However, as noted on GoNintendo, there's been instances where games were incorrectly dated on the site, and would end up coming out a week or two later. Oops.
Pending official word from Nintendo (via press release), I suppose we'll just have to wait and see what Thursday will bring.
Thanks to Robdog511 for the tip!