My neorest 500 smells we have had it for 4 years. I am wondering what can be done. we love the toilet.

Its the deodorizer built into the seat that's not functioning, contact Toto customer service and they can sell you the replacement part. Or take off the seat and send it to them to replace.

Smells usually come from the tank and not the bowl.
Buy tank deodorizer from local store located near toilet brushes.
http://secure.willert.com/images/bf_wire.jpg
Deodorizer hangs inside tank. make sure it reaches the water.

You can also drain and clean the tank using CLR calcium lime and rust remover.
The CLR and gunk are fine for flushing away as long as the gunk doesn't clog the flush holes that let water flow into bowl.
http://www.fixya.com/support/r6633961-toilet_doesnt_flush_water_just_spins

Sewer line can also cause of odor.
If the toilet bowl is not full of water, or if nearby drain is not filled with water, or if toilet is not sealed tight against floor, or if toilet appears to have dampness visible around base, or if a vent pipe terminates behind a wall instead of on the roof: these things can cause sewer air to enter room.