Update: I just put the code into this github repo for easier access https://github.com/sharpgit/admin-only-payment
Download the Zip File Below (or get it from github) and you will be on your way to allowing payment methods for Admin Orders.
This module will add a drop down box to payment methods that will allow you to enable it for admin orders. If the payment method you use does not have this drop down you will need to edit the modules /etc/system.xml file and add in a node that corresponds to your payment method.
Here is an example of adding a new payment method to the module. I edit the file /app/code/community/Sharpdot/SharpAdminOnlyPayment/etc/system.xml
Note: I am working on updating this module to automatically recognize all payment methods, so that editing the system.xml file will not be required in the future.