You let them go free. "It is better that ten guilty persons escape than that one innocent suffer."

If you actually have so many people committing crimes that there are actually too many guilty people for the courts to properly try, you have a societal engineering problem, not a courtroom efficiency problem - you need to get people to stop committing those crimes in the first place, since clearly the justice system isn't working as a deterrent. There are lots of options, including changing social conditions, reclassifying the behavior at issue as not a crime, etc.