Can I customize what goes into the "Messages" indicator? For example, I only want to see my work Enterprise Server emails there. I want to remove Missed Calls, New SMS, new Yahoo & Hotmail email alerts and all other alerts from this one folder/indicator/application (I'm not sure what to call it, it's the Mailbox icon on the desktop).

If not, can I create a seperate Mailbox Folder just for my work emails?

Thank You!

No. Messages icon is a catch ALL for messages.

Look for a 3rd party app called Entourage I believe which will create a BES mailbox icon, so you can then hide the messages icon and use the individual mailbox icons for your different email accounts.

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.