You should only use ispropyl alcohol of 90% or more. It is a pure substance that will evaporate without leaving anything behind, and it costs less than a dollar. Don't use so much alcohol that it runs all over your board. Don't use nail polish remover as it will leave behind all the extra ingredients, like perfume. Also don't touch the GPU with your fingers, even if you wash your hands first, you will leave behind oils.
I use Arctic Cooling MX-4 and apply it with small applicator brush (ironically, like a nail polish brush) that I clean with alcohol and dry first. Cover the entire GPU surface (the silver part). Just think that the ideal situation would be metal on metal, but due to imperfections in the GPU surface, the thermal paste is needed to fill in those micro-dips and valleys. So use a very, very thin layer, to the point where you can almost still see the lettering on the GPU. Clean off anything that goes over the edge or onto the board, a Q-tip works well for that.