My windows are stuck in the down position, except drivers front, the lock window button isn't engaged and the windows actually went down on their own.
You'll have to do a little troubleshooting to find the cause. I would start looking at power window control switch module in your driver door armrest (assuming it has one, you didn't specify what type of vehicle you have). A short or an arc may have caused them to not function. You didn't say if the key was in the ACC/ON position when this happened, as typically the switch isn't powered with the key off. Post 1999 cars the key fob can also roll down all the windows by holding the unlock button for several seconds, but that wouldn't stop the windows for working and you say yours are stuck. If you have a meter and a wiring diagram you could test your switch module, but short of that just get a replacement one from a pull-a-part or auto parts store and switch it out.
2006 Toyota Forerunner SR5, V6 and the key was turned on at the time.
Have you been able to get any of the windows back up, with the driver door switches or the individual switches at each door?