Operations manager is the preferred method for monitoring you BizTalk Application.
We recently released BizTalk Managgement Pack for Operations Manager 2007. You can use this management pack to monitor BizTalk 2006, 2006 R2 and 2009.
You can get it at:
http://www.microsoft.com/downloads/details.aspx?FamilyId=389FCB89-F4CF-46D7-BC6E-57830D234F91&displaylang=en&displaylang=en
