1.) Use and on TEXT/NOTICE/CTCP event (depending on how the message is sent, sorry don't use Quakenet) to ignore 'keywords' in the welcome message, or the nickname entirely.
2.) The color tab in the Address Book or the /cnick command will do what you're asking.
3.) Open the options dialog (ALT+O), goto Display -> Options. Click on the 'Tray' button and check the 'Place in tray when minimize' checkbox.