This list was originally created by the Microsoft BizTalk support team. Feel free to add to it.
Use Group Hub in BizTalk Administration to check for suspended and dehydrated instances. This will also give you a chance to investigate why these items are suspended/dehydrated.
Do not let suspended instances accumulate. They should be handled promptly by either being terminated or successfully resubmitted. If these items reach in the thousands, performance can be impacted. MsgBox Viewer also breaks down the suspended instances by host.
Confirm the BizTalk SQL Agent jobs are executing as they should. Pay special attention to the Backup BizTalk Server job and make sure it runs successfully. In case of a disaster recovery, you may need these database backups. For a description of the SQL Server Agent jobs, refer to the following KB:
919776 Description of the SQL Server Agent jobs in BizTalk Server
http://support.microsoft.com/default.aspx?scid=kb;EN-US;919776
Another important place to find a huge amount of BizTalk related articles is the TechNet Wiki itself. The best entry point is BizTalk Server Resources on the TechNet Wiki. Read suggested related topics: