Download the Zip File Below and you will be on your way to allowing payment methods for Admin Orders.
This module will add a dowp 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

//This is the origional code for a bankpayment. I just need to duplicate this and adjust the code to reflect a new payment method.
<bankpayment>
	<fields>
		<admin_active translate="label">
			<label>Admin Override Enabled</label>
				<frontend_type>select</frontend_type>
				<source_model>adminhtml/system_config_source_yesno</source_model>
				<sort_order>1</sort_order>
				<show_in_default>1</show_in_default>
				<show_in_website>1</show_in_website>
				<show_in_store>1</show_in_store>
		</admin_active>
	</fields>
</bankpayment>
//This is the adjusted code for a new payment method. This is a made up payment method, with the code "sharppayment". You would just need to substitute your payment methods code.
<sharppayment>
	<fields>
		<admin_active translate="label">
			<label>Admin Override Enabled</label>
				<frontend_type>select</frontend_type>
				<source_model>adminhtml/system_config_source_yesno</source_model>
				<sort_order>1</sort_order>
				<show_in_default>1</show_in_default>
				<show_in_website>1</show_in_website>
				<show_in_store>1</show_in_store>
		</admin_active>
	</fields>
</sharppayment>

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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.