Hi , 


Using Certificates with SOAP Services: 

The following example illustrates the last step of the previous procedure and works with the sample WSDL file in Understanding the Generated Code. This example assumes that you previously generated a certificate with a Unique Name of DocSampleCert.
docSample.DocSamplePort stub = new docSample.DocSamplePort();
stub.clientCertName_x = 'DocSampleCert';
String input = 'This is the input string';
String output = stub.EchoString(input);
There is a legacy process for using a certificate obtained from a third party for your organization. Encode your client certificate key in base64, and assign it to the clientCert_x variable on the stub. This is inherently less secure than using a Salesforce certificate because it does not follow security best practices for protecting private keys. When you use a Salesforce certificate, the private key is not shared outside Salesforce.
Note
Do not use a client certificate generated under Setup, in Develop | API | Generate Client Certificate. You must use a certificate obtained from a third party for your organization if you use the legacy process.
The following example illustrates the legacy process and works with the sample WSDL file in Understanding the Generated Code.
docSample.DocSamplePort stub = new docSample.DocSamplePort();
stub.clientCert_x =
'MIIGlgIBAzCCBlAGCSqGSIb3DQEHAaCCBkEEggY9MIIGOTCCAe4GCSqGSIb3DQEHAaCCAd8EggHb'+
'MIIB1zCCAdMGCyqGSIb3DQEMCgECoIIBgjCCAX4wKAYKKoZIhvcNAQwBAzAaBBSaUMlXnxjzpfdu'+
'6YFwZgJFMklDWFyvCnQeuZpN2E+Rb4rf9MkJ6FsmPDA9MCEwCQYFKw4DAhoFAAQU4ZKBfaXcN45w'+
'9hYm215CcA4n4d0EFJL8jr68wwKwFsVckbjyBz/zYHO6AgIEAA==';

// Password for the keystore
stub.clientCertPasswd_x = 'passwd';

String input = 'This is the input string';
String output = stub.EchoString(input);


http://www.salesforce.com/us/developer/docs/apexcode/Content/apex_callouts_client_certs_soap.htm


Regards,
Ashish