Nearly every time I've had to deploy code to certain production orgs I've done so with a feeling of dread, purely because I've had to go in there and disable the scheduled Apex Jobs before doing anything and then afterwards, I need to set them up again. This is a definite pain point as you need to be sure to set everything up correctly, and as I learned recently the system won't even warn you if you set up one job twice, even specifying the same time on each setup!
I've just performed a deployment to an org which has 7 batch jobs that I usually have to stop — this time I did a bit of research first and noticed in the API docs that there's a 'Paused' status which can be applied to such jobs. I thought that maybe I could set the jobs to have this status through some ad hoc code, but before getting around to that I hit the button to validate the deployment. You know what? I got a green light, without disabling or stopping any of these jobs. I've looked through the notes for Winter '12 and couldn't see anything regarding this, but have Salesforce made a change to allow deployments while jobs are scheduled? It seems that way, and I truly hope that I'm correct in this assumption!