applying conditional tags dynamically

I would like to know if there is any option to apply conditional tags dynamically to the output. This is the scenario. There is an application, which might have various options. These options will be integrated based on the customer requirement. For instance, Customer A might need some options which should be hidden form customer B and customer B need some options which should be hidden from customer A.  Now based on the customer requirement, is there an option by which the same HTML Help  can be configured for Customer A and Customer B since many of the options are common? Please note that t applying conditional tag has to be done on the output, and not before generating the HTML Help.