NADA also lists motorcycles. You'll find the price between the two listings is usually not the same. Kelly Blue Book reflects dealer asking price and 'appraised' value, where NADA is based on member dealers reports of what they actully sold that model for in a certain period of time, or certain number of sales. With cars and high volume bikes like Harleys NADA is more accurate, but with low-volume vehicles like metric cruisers KBB is probably a better guide because the NADA number is based on older or too few sales.
As for popular accesories like aftermarket pipes, windshields, and saddlebags (and modifications you have a receipt for) the rule of thumb is that they increase the value of your bike by no more than 1/3d of what you paid for them. Oddball mods (like a hot pink paint job or a picture of your girlfriend on the tank) usually decrease the value of your motorcycle, as they appeal only to you and to no one else.