Yes, powering down at night can save you money, and it can reduce your carbon footprint but it sounds like you are trying to use this as a method of securing your network which i would not suggest.
As far as powering down your systems, if you have a budget then use it. If you have management software, use that too. Many large networks use some sort of management software, either SMS or something similar. There are always tools available with this. Some good SMS add-ons can be found here:
http://www.1e.com/Downloads/Index.aspx (no affiliation aside from that we use the software). These tools give you the option to only shut down computers which no one is logged into, or you can be more strict and force systems to shut down at a specific time, it is very flexible.
If you do not have any such thing and you do use AD then simply get creative with your policies. You can use power management policies which were mentioned earlier such as EZ GPO
http://www.energystar.gov/index.cfm?c=power_mgt.pr_power_mgt_ez_gpo or you can get creative with your logon scripts. Just be sure to test them first.
If you are simply trying to thwart viruses maybe you should look into a unified threat management appliance which can stop them at your gateway.
