Is it possible to disable notification generated by Mail.app for a certain set of folders?
For e.g. if have
Inbox > fol1 &
Inbox > fol2, I want notification from
Would this be possible with growl somehow?
You should be able to do this by setting up Rules in Mail.app that filter on the criteria you desire and then run an AppleScript that triggers a Growl notification. Rules are setup in Mail.app under Preferences…->Rules.
Growl can be called from AppleScript as shown here.