The emission standards (Euro 1/2/etc.) basically determine the taxes that you'll have to pay and if you'll get a "Umweltzonen-Plakette".

The "G-KAT" sticker is no longer of importance, but the "Umweltzonen-Plakette" becomes more and more important as many cities are establishing the "Umweltzonen" which you are only allowed to enter with the mentioned sticker.

Regarding the price: The price on the window can ALWAYS be negotiated, be creative*; and in Germany: "Bargeld lacht".

The prices negotiated in the end is the final price, no further taxes or fees. Next point where you'll have to pay is the insurance and the taxes.

What type/manufacturer are you looking at?

*=you're not on a bazar, but starting with a low offer (e.g. minus 30%) will give you a good basis, the used car dealers are currently under pressure because of the "Abwrackprämie" that supports mainly the sale of brand new, small cars (such as the VW Polo or Golf).