Stomatitis is a frustrating problem.
Antibiotics can help keep the bacterial load down. There has been some success with low dose doxycyline use as it can have an anti-inflammatory effect as well.
In a recent study, it was noted that 88% of cats with stomatitis were also shedding calici and herpes virus. At this time, we do not know if there is a connection or not. However as growler has mentioned - food and diet may be helpful. Lysine supplementation is a safe, holistic method to address the potential presence of herpes.
Other options such as cyclosporine have been suggested but more information is needed on this disease unfortunately.
I have also prescribed oravet and had some success with it. Oravet is an electrically charged wax polymer that binds to the teeth, helps reduce plaque and reduce the bacteria. It is easy to apply and is used once a week. It is currently being marketed as a dental sealant but may have some applications in the treatment of stomatitis. Link:
Oravet
Unfortunately dental extraction is still the recommended treatment of choice for many cats and appears to have the best long term effects. However as growler mentioned, some cats still have problems. Those that do - CO2 laser ablation therapy is recommended. Here is a excerpt from a lecture on stomatitis with regard to dental extraction response: "The response to tooth extraction ranges from complete resolution of inflammation (60%), minimal residual inflammation and no oral pain (20%), initial improvement requiring continued medical therapy to control clinical signs (13%), to no improvement (7%)." - Dr. Alexander Reiter, University of Pennsylvania School of Veterinary Medicine at the Atlantic Coast Veterinary Conference 2008.