1. A monitoring system for virtual application environments comprising: at least one physical machine executing a first operating system; at least one virtual machine operating on at least one of the at least one physical machines, each such virtual machine operating a second operating system; and an agent program operating on each of the at least one physical machines, where, each agent program is operable to obtain a first set of metrics from the first operating system, such first set of metrics including metrics in respect of each virtual machine as viewed by the first operating system, and operable to connect to the second operating system of each virtual machine hosted on the physical machine the agent program operates on and obtain a second set of metrics in respect of the virtual machine from the second operating system, the agent program further operable to communicate the first and second sets of metrics to a manager program.