Is there any way i can set flag or change the color of the subject line of a mail sent from unix. ?
Should that be in your own mail viewer or at the receiver end?
Anyway you can use mutt:
With vim and mutt you can fix everything, f.ex. adding "X-Priority: 1" to a outgoing mail. Colors of the subject line in your mutt can be done by settings in the .muttrc file, like
color index brightred default "~h 'X-Priority: 1'"