Howto Create Custom Payment Method in Commerce Server

Creating a Custom Payment Method For CS 2007
http://msdn.microsoft.com/en-us/library/bb219356(CS.70).aspx
Another good post about extending order system entities such as OrderForm, .. etc of CS 2007 is at:
http://blogs.msdn.com/sathishcg/archive/2006/11/08/extending-commerce-server-order-system.aspx

How to extend Commerce Server Payment Methods and Shipment Methods for CS 2007
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createing a custom payment method, explained with screenshots, by technicalmultiverse

Custom Payments in Commerce Server 2009, by jthodges
Creating a Custom Payment Method For CS 2009
http://msdn.microsoft.com/en-us/library/dd328095(CS.90).aspx
Also CS Guy provided a blog entry about creating a new payment method
http://commerce-server-guy.blogspot.com/2009/04/adding-new-payment-method-in-commerce.html
Although it is not detailed but helpful information about extending order sysetm for CS 2009. Steps involved in extended commerce server 2009 Systems,
by Ravi KANTH

Summary of the procedure from MSDN: To create and configure a custom payment method

  1. Create a pipeline component that processes the payment. For more information about how to perform this step, see How to Create a Payment Processor.

  2. Use the Pipeline Component Registration tool (PipeReg.exe) to register the pipeline component. For more information about how to perform this step, see Building Pipeline Components.

  3. Create a new pipeline that includes the payment processor that you created and registered in steps 1 and 2. For more information about how to perform this step, see How to Create a Custom Pipeline.

  4. Update the Web.config file to reference the new pipeline. For more information about how to configure a pipeline in the Web.config file, see pipelines Element.

  5. Follow the procedure in the topic How to Create a Payment Method to create the payment method. For the payment type property, select one of the payment types that start with the word “Custom”.

Beware when adding a new payment type, order of class definitions and tables in OrderObjectMappings.xml have to be the same, otherwise it does not work.
http://social.msdn.microsoft.com/Forums/en-US/commserver2009/thread/cac83579-4fc9-44fd-97c0-13cb1ec7fbad

Do not externalize your web.config sections, you may face issues with order system api.
http://social.msdn.microsoft.com/Forums/en/commserver2009/thread/77aefb7a-5547-4489-a3c9-6292f48e7221

Commerce Foundation Operation Sequences