Each boss often has a higher chance to drop rare resources. They also guarantee Warframe blueprint parts, and may also yield weapon parts and/or blueprints.
Completing the objective of an Assassination mission has a chance to place a Death Mark on the Tenno, which in turn gives a chance to face certain random bosses.
Trivia
Though the Lotus will sometimes tell the player not to let the assassination target escape, none of the bosses will attempt to flee.
It has been noted that occasionally, if Zanuka is killed first, Alad V will attempt to flee the boss room. [citation needed]