Mods don't necessarily decrease the value of the car. But they never increase the value of the car as much as the amount spent on the mods. And they CAN make it more difficult to sell the car, since you are giving up that portion of the market who prefer a stock or close-to-stock car. (And difficult to sell may mean that you have to settle for a lower selling price.) OTOH, you MAY find someone who wants a car with exactly the mods you have installed, in which case you may get significantly more for your car than you would without the mods. It introduces an element of chance into the resale question.
I would think that the more common the mods, the easier it is to find someone who is willing to buy a car with them. The most common mods, of course, are probably wheels, intake, exhaust, headers, springs, struts, and sway bars. Some mods - most notably the supercharger - aren't as common just because they're more expensive than other mods, but I would think that a SC would add significantly to the value of the car.
I would think that most folks make mods because they like the car better that way, and don't care what their effect on the car's resale value is. If you only focus on cost-justifying the mods, you would probably conclude that your best bet is to leave the car stock. If that's not what you want, well, then do what you want!
