Different payment methods for different stores

Create a custom module. 
Let’s call it Ankur_Pay. 
Create these files: 
app/etc/module/Custom_Pay.xml with this content 

<?xml version="1.0"?><config>
    <modules>
        <Ankur_Pay>
            <active>true</active>
            <codePool>local</codePool>
            <depend><Mage_Payment /><Mage_Paypal /></depend> <!--add here all the payment modules you have so this module will be loaded last-->
        </Ankur_Pay>
    </modules>
</config>

app/code/local/Custom/Pay/etc/config.xml 

<?xml version="1.0"?><config>
    <modules>
        <Ankur_Pay>
            <version>0.1.0</version>
        </Ankur_Pay>
    </modules>
</config>

app/code/local/Custom/Pay/etc/system.xml 

<?xml version="1.0"?><config>
    <sections>
        <payment>
            <groups>
                <ccsave><!-payment method starts here -->
                    <show_in_default>1</show_in_default>
                    <show_in_website>1</show_in_website>
                    <show_in_store>1</show_in_store>
                    <fields>
                    <active><!-- from here-->
                        <show_in_default>1</show_in_default>
                        <show_in_website>1</show_in_website>
                         <show_in_store>1</show_in_store>
                     </active><!-- to here-->
                      <cctypes>
                        <show_in_default>1</show_in_default>
                        <show_in_website>1</show_in_website>
                         <show_in_store>1</show_in_store>
                     </cctypes>
                  </fields>
                  </ccsave><!-payment method ends here -->
            </groups>
       </payment>
     </sections>
</config>

Now you need to add in your file a section like the one marked between ‘<!-payment method start here -->’ and ‘<!-payment method ends here -->’ for each payment method you want to see at the store view level. and for each payment method you need to add for each field that you want visible at all levels a section similar to one marked between ‘<!-- from here--> <!-- to here-->’. and just keep the tag names. 

I hope I was clear enough. 


or you can make a condition on payment/method.phtml

if(WEB_ID!=3){array_shift($methods);}elseif(WEB_ID==3){$methods;unset($methods[1]);unset($methods[2]);unset($methods[3]);
}

Enjoy....