Cecile finds out that the Flash is Barry Allen, and tries to use that to help him win the case (figuring the jury wouldn't find against a guy who is saving his second wife from being murdered by the guy who murdered his first wife), but Barry outsmarts her and gets plastic surgery to disguise his identity. The Reverse Flash then seems to show up alive!
Then, in Flash #348, a verdict is reached - guilty!
However, as it turns out, the return of the Reverse Flash and the guilty verdict were both caused by the villain from the future, Abra-Kadrabra, who pretended to be the Reverse Flash and also hypnotized the jury into finding the Flash guilty.
As it turned out, though, one of the other jurors was intent on fixing things. You see, this juror was also from the future, but while he looked like a middle age man, he was actually someone close to Barry...
Yep, Iris wasn't actually dead! You see, years earlier, we had learned that Iris was born into the future and was sent into the past. So when she died, her birth parents just rescued her soul/essence/whatever and transported it to the future to a new body. They then sent her back in time to clear Barry's name. She suceeded and, once Abra-Kadabra's involvement was revealed, the Flash was cleared of the guilty verdict.
Of course, by this point in time, Barry had just went off into the future to live with the resurrected Iris happily ever after, as the Flash series ended with Flash #350.
Oh, did we say "happily ever after?" Oh, right, yeah, about that, right after this, Barry had to travel back to the present because of Crisis on Infinite Earths and he died saving the universe in Crisis on Infinite Earths #8, which came out a mere month after Flash #350.
But hey, at least he wasn't really convicted of murder!
Time will tell what fate awaits the TV version of Barry Allen in his trial.