especially for flash games i have some half-baked ideas that might work (security through obscurity):
load a special highscore swf during runtime. the name of this should be randomized (server knows the name via sessionid)... make a little vm in as3 that handles the scoring of the game (verification, adding of score points etc). the vm uses different algorithms to encode the highscore (to be valid) and decrypts/encrypts each line of its byte code before/after execution. the vm is in the highscore swf loaded during runtime. by randomizing the algorithm of encoding etc. it is very hard for a hacker to reverse engineer this. the bytecode for the vm could be delivered within images. the images are encrypted sessionid dependent... (this might work without a vm too)
during gameplay one could ask the server for some random numbers. these may be used to trigger some score giving points. the "score history" has to be submitted along with the highscore. the highscore is signed with the previously submitted random numbers... the random numbers submitted during gameplay could be used to verify the gameplay time too.