As of 2007A PL35, it is possible to do a reconciliation between multiple BPs, including between a Customer and Vendor.
In Business Partners > Internal Reconciliation > Reconciliation
Choose "Manual" and then check the box for "Multiple BPs"
This allows you to choose any number of BPs and view their documents. It is even possible to reconile partial amounts on documents between the BPs.
For example, if I do business with a company that is botha customer and vendor (2 seperate BPs) I can reconcile an A/P Invoice for $50 against an A/R Invoice for $100 between the two BPs of that same company. This will leave $50 open on the A/R Invoice. On the document, you can drill into Applied Transactions and actually see where that the applied amount came form the multiple BP Recon.
It's also helpful to print the recon screen when it is done, because it gives nice visibility into which documents were reconciled together and what the remaining balance is.
Hope some of you find this valuable.