Hi Portia,
I'm going to try and answer each of your questions 
Q: What is the difference between virtual machine and physical machine?
A: A VMware Virtual Machine (VM) simply consists of files who represent the physical hardware that is normally in a physical machine (Hard drives, BIOS and a VMware configuration file). The memory and cpu time are not dedicated to one server but are divided by the VMware Hypervisor which is on top of your virtual servers.
This way you are working more efficiënt because machines not doing anything would be a waste of resources in the physical world. The possibilities for storage are expanded as well, since you aren't bound to local storage but able to store your machines on a NAS or even a SAN if your budget allows that.
Q: How can i identify whether my application is running in a Virtual Machine or not?
A: I can't fully understand what you are saying here. Do you want to know if your application is capable of running in a VM, or identify if an application is currently running inside a VM?
Q: How can I get all the VMs from a physical host?
A: As with the previous question, what exactly do you want? Do you want to convert all your physical machines to VM's or trying to move VM's from an existing ESX Server to a different or multiple physical machines?
Q: How can I differentiate physical OS and Virtual Machine OS
A: There is as far as I know, no difference between the OS on a physical machine and on a VM. You install the OS (Whatever that OS may be) on a harddisk. In the physical world mostly on DAS (Direct Attached Storage) and in the virtual world (VMware) on a virtual harddrive presented as DAS to the VM.
Q: Can I identify current machine is a Virtual machine ?
A: If the OS is booted up, only the VMware Tools application could "reveil" that the machine currently logged on is a VM. Correct me if I'm wrong.
If you created licenses on IP address, it's possible to do a P2V (Physical to Virtual) so the IP address remains the same. I don't know if your licenses will work but as I can read in your post, it's unclear if what you are doing isn't illegal. I suppose that if the license is IP-based, it's registered per-machine.
You will have to test that on yourself.
Hope this helps you!
René
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because i created license based on IP ADDRESS
Really ? - this is an open invitation to cheating 
I guess you mean the MAC Address instead.
There are several ways to detect if the app you want to protect is running inside a virtual machine.
Have a look here for example http://www.codeproject.com/KB/system/VmDetect.aspx
and read about "blue pill" and "red pill" in google.
Read http://chitchat.at.infoseek.co.jp/vmware/backdoor.html#top
Also scanning the virtual BIOS for the Vendor is useful.
Anyway - to detect if your app is running inside a VM I would use more than one procedure
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