Applications halting overnight

Have you checked the event viewer to see if there are any events relating to the shutdown?

You might want to run a chkdsk on the drive you are downloading to in order to make sure it's ok. While you are at it, use speedfan or HDTune to check the SMART status of the drive.

Nothing particular in the event logs. I have some errors pointing to issues with a trusted certfificate list but internet searches indicate it can be ignored.

Have you run chkdsk or checked the SMART values for the drive you are downloading to?

might have been windows update... there was a patch pushed like 2 days ago... this would explain your programs being gone... was it back at the login screen or just sitting at the desktop if it was at the desktop do you have auto login turned on?

Windows 7 is setup to automatically do a lot of stuff by default. While nice for the average user, it can sometimes be really annoying. I stopped using sleep mode on my HTPC because it likes to wake itself up to perform tasks in the middle of the night. Maybe one day I'll turn off all those midnight tasks so my computer stays sleeping instead of having to power it down.

Check your task scheduler and see what is happening in the middle of the night. I wouldn't be surprised if Windows Update went off and rebooted your computer.