When I call about a microchipped animal we find stray, the microchip company can tell by the number which company it comes from and just tell me who to call
PetWatch allow registration of all types of North American chips but if I recognise it as a HomeAway chip, I call them not PetWatch and they don't share numbers so as I have cats with 3 different chips, I registered them with their respective chip companies as well as PetWatch (free).
http://www.24petwatch.com/preregister-petowner.aspx
home again also offers registration of other chips
http://public.homeagain.com/faq.html#needmicrochip
Most shelters or vets will call their chip company first so call around and see what shelters in your area use before paying for multiple companies, but if it is free registration - it can't hurt to register on all of them.