I'm firmly in the make it ugly camp.

My bike isn't a "beater" and it isn't ruined, it probably works better now than the day I bought it. I mean really, no one has to know if your bike is expensive or not, or what type of components you have. Why do other people have to know that?
I can assure you that painting a bike flat black and removing (or hiding) component logos does not change the performance of the bike at all. All it does is give you peace of mind that your bike wont attract too much attention.