To a degree.
Disable call logs via the Phone/Call Log->Options->Call Logging. Set it to None.
You can separate SMS/MMS so they have their own icon and only appear under that icon via Message->Options->General Options->SMS and EMail Inboxes. Set to Separate.
As for BES mail, you can either get your BES admin to enable the BES icon or use Empower BES Mailbox. Won't make a difference in Messages but it will create a BES mail icon.
You can't control what email arrives in Messages nor can you prevent Messages from receiving PIN messages or storing saved browser requests, saved browser pages, etc.