Yea, usually if they're in-progress for more than a several minutes, you have a problem. Stuck overnight would be a definite problem. I would first try cancelling them, you can do this with the "cancel all" or select individual ones in the Config Management / Transfer Status and cancel them. If that doesn't work, restarting the services as Jiri pointed out. Using the Orion Service Manager is the best way to do this, just "stop everything" then "start everything" once everything has stopped.
One thing I've noticed, if you have RTCD configured and some of the auto-download jobs are stuck, it seems to make download jobs like these get stuck easier. Sometimes killing off any "ConfigAutoDownload.exe" jobs that have been stuck in Task Manager for awhile can help.
If you're pretty sure you have a bunch of stuck "ConfigAutoDownload.exe" jobs and don't want to kill them all manually, doing the following from a DOS prompt will kill them all. Wouldn't recommend it if you believe a large # of jobs might be processing at that point in time. This only gets rid of downloads started by RTCD, not those done through NCM on the webpages or via jobs. There is not a direct correlation between RTCD jobs and those done manually.
'taskkill /F /IM ConfigAutoDownload.exe'