If you have orchestrations or messages that are marked as ‘Suspended (resumable)’ after the crash, just resume them and they will continue as if the crash never happened. In the case of orchestrations, they will resume from the last MessageBox persistence point (see http://geekswithblogs.net/HenriKluijtmans/archive/2009/12/18/persistence-points-in-biztalk.aspx).
If you are looking for an simple and efficient way to archive BizTalk messages, you should take a look at the BizTalk Message Archiving Pipeline Component from Atomic-Scope (shameless plug) – see http://www.atomic-scope.com/ for more information.
Nick.