A common question that resonates through the CRM customer base is allowing for filtered lookups between entities. I am currently in the final stages of a client who wanted this functionality between some custom relationships set between contacts and opportunities and another custom entity and opportunities. Here are a couple of resources on the two:
Application Based
http://www.stunnware.com/
Code Based
http://crm.georged.id.au/post/2008/02/16/Filtering-lookup-data-in-CRM-4.aspx