There are two types of penetration in lol flat and percent and can only bring armor down to 0 giving you true damage. Armor reduction from items like black cleaver and Starks fervor can bring armor below 0 giving you bonus damage on top of true damage.
The order of operation for calculating is reduction>flat penetration>percent penetration
So in order to gain bonus damage you must have more armor reduction than they do armor other wise armor reduction will serve the same function as flat armor penetration

There is malady now has mr reduction and abyssal scepter has reduction aura Also a lot of heros have mr reducing skills/passives fiddle amumu karthus and some others
Here's a good link for mechanics in the guides forum
http://www.leagueoflegends.com/board...ead.php?t=3287