A while ago I played a game of Puerto Rico with all of the buildings from Expansion II: The Nobles. One of the players pretty much had a run-away game using Villa + Jeweler, and we were pretty much at a loss as to how to stop it.
With the new expansion, each time the Colony Ship is refilled, one of the colonists is replaced by a Noble. Each Noble is worth 1 VP at the end of the game, but more importantly they can trigger other buildings.
Mayoring became the hot action of the day, and the Corn player pretty much forsaking all building until they hit 6 doubloons + quarry + building privilege to buy the Jeweler (they were pretty much Captaining the rest of the time, if you're curious). The Jeweler gives you 1 doubloon in the Craft phase for each Noble you have, which isn't exactly overpowered given it's cost, until you bring Villa into the picture.
Within two turns of Crafting, the Jeweler player had enough money to buy a Villa, which lets you take an additional Noble from the supply when anyone mayors. Thus, if he would Mayor, he could actually get two Nobles, one from the ship and one from the supply.
This is pretty much where the game got silly, because every Mayor gave him +1/2 endgame VP which translated into +1/2 more doubloons during the crafting phase, which, in turn let him buy the Royal Gardens (+1 VP for each noble at end of game) and other big-ticket items quickly.
I'm not sure which part of the combo is broken, though, the Villa or the Jeweler? The Jeweler is more expensive than the Factory, but rewards you for something you already want to do (collect Nobles). The Villa simply gives you an extra Noble each turn (1 VP a turn isn't unreasonable), but put them together and the free money starts to roll in.
Short of all other players buying Villas as soon as someone buys a Jeweler, or applying a house rule, how can you counter this? Or have others seen that Jeweler + Villa is degenerate enough to simply not allow both buildings in the game at the same time?