Junior General has a simple set of Medieval Castle siege rules. The site also has links to appropriate paper figures, castle models and siege equipment.
From the Perfect Captain comes Spanish Fury: Siege, a board game about besieging a 16th century town or fort.
Ryan Scow offers a set of free medieval siege rules.
Matt Fritz has these simple set of free wargamesrules for recreating the Siege of Tenochtitlan. He uses them with his students — a great idea for both wargaming and learning! It inspires me to try similar things in my classroom.