I put in cliffys, plastic protectors, etc., but other than that I leave my machines stock. Just a personal preference though, for some people a lot of the fun are blinging things up. If I ever get a Tron I am putting in the tron arcade mods though, as that is just way cool.
The only time I would ever have a problem with it is if I was looking to buy a machine that had a bunch of non-reversible mods on it.