At a minimum, adding such a legend to your checks should prompt payees to negotiate them sooner. It could have a chilling effect on third-party banks accepting the checks for deposit once that 90-day window is closed, since those banks would not know whether the checks would be honored when presented to the drawee bank.
Your bank is likely to take a dim view of such a legend, however. In today's high-volume check processing environment, check dates are rarely looked at, and your bank probably will not be willing to say it will bounce checks that are presented after any particular "age" is reached. I can imagine that some banks with positive pay systems (overly simplified: the bank has a list of the checks issued by its larger business accounts, and won't pay items not on the list) might be able to catch checks that are older than three (or six or twelve) months old, and bounce them. You should ask the bank about its abilities in this area.