There was a domain name change, but the blog post is still available:
http://geodatabase.net/wp/sql-server-2008-spatial-indexes-and-arcsde-9-3/
The content of that blog post, and this forum discussion, is pretty good, but it all is nearly 2 1/2 years old. ArcSDE has changed some and SQL Server has had lots of improvements to its spatial support. If you are truly running SQL Server 2008 with no service packs and ArcSDE 9.3/9.3.1, I think there is likely a larger issue that needs to be discussed more than tuning spatial indexes.
Good luck!
Thanks for the link and feedback. For this issue, both ArcGIS and Geodatabase are 10.1 sp1, MSSQL is 2008R2. We imported a parcel base feature class of ~300,000 polygons, stored in sde_binary, and it performs just fine, as it always has since the days of MSSQL 2000 and 9.something ... but an exact copy of it with geometry storage, display and query performance is unacceptable, almost shapefile slow. The layer envelope is not the issue. I can't find any discussion on the support forums etc. or guidance in online help. Any suggestions?
Thanks!