I'm building a new house with Dick Clark Architects and it generally has pretty standard Tyvek weatherization details. We're using DuPont Tyvek Drainwrap along with DuPont FlexWrap for sills, and Straightflash for jambs/heads of windows, then blanketing the whole house with 3/4" rigid foam. The cladding is a mixture of Wood Siding, Hardie Siding, and Stucco. (Side note, I'm a big fan of the Tyvek products, but you must use ALL their products together in a weatherization system.)
The windows are a mix of Ram (Thermally Broken Commercial Aluminum), and Andersen 100 (high performance composite windows). All the windows are installed in the standard nailing flange method, but I've got one window that has a funky recessed detail.
Here's the video we made of the process. Matt Risinger - Risinger Homes in Austin TX. www.risingerhomes.com
For more pictures of this recessed window install visit my blog www.risinger.blogspot.com