Both of my cats were microchipped at the shelter we adopted them from and it didn't seem to bother them too much. The price of the microchip was included in their adoption fee ($75 for both of them!
).
With the dogs, I had them microchipped while they were under for their spay and neuter. I believe it was around $35? They never knew they were microchipped, and it gives me the piece of mind knowing they are.