Applications should have a setting that allows the user to turn it on or off and set the schedule. For something like an antivirus program I want to check for updates very often, but for something like VMWare Player once a week is plenty for me.
That depends on what it is (how much I trust it), and how much spare CPU power and RAM I've got. I leave Anti-virus updates turned on, always. On a weaker system, I turn most of the other stuff off, and perform manual checks at my convenience. If it's from Google, I turn it off and check manually, or just install fresh, making sure to inspect privacy settings afterwards.