You should be able to do this from REST API in vCD or PowerCLI (i think). REST API pseudo code would look something like this:
start script (input is org name or ID)
login to REST API as System Admin
use the query service to get a list of all vApps for a specific organization (you might have to parse multiple pages of results depending on how many vApps there are)
for each vApp in the array
- get a list of All VMs in the vApp (query service or get on the vApp reference should give you the list) ... again parsing for multiple pages
- for each VM in the new array
- do a get on the VM (obtains current configuration and state information)
- if (power state != off) then issue power off API call to it
- move to next VM
move to next vApp
Logout of REST API
end script