Best bet is to negate Flash's speed advantage. Guys like Reverse Flash, Zoom, and the Top are all about his level of speed. Other villains have to be more creative. Captain Cold will at times project cold fields around Wally that would stop him dead in his tracks. Someone with The Alchemist's weapons turned rain into either acid rain or sharp scraps of metal, which cut Wally up like sushi.
Normal street level thugs don't stand a chance, but certain people (like the ones I've mentioned) have done it.