For me, they decrease value in a couple scenarios. First, if it ruined the original part. Like powdercoating the coin door...ugh. If I have to go out and buy a replacement for it, value is lowered. Also, if it replaced the original part and the original part that was replaced is not included. Case in point, aftermarket translites. I want the original, don't care in the slightest about a home brew one that someone thinks "looks great", so once again if the original is not included and I have to go out and buy one, value is lowered.
Outside of color dmds, most other mods are just part of the package for me and like others have said, I don't attribute any value to them specifically. I have a dollar amount in mind for the game as a whole, if the sale number is at or below that...we're in business.