hem... one thing is helping you to create certs and key for a SSL protected webserver, quite another to help you managing a credential store (I really don't have time for that). You have problems on finding out what OpenSSL is and want to manage X509 ? Really ? Maybe it's time to read some docs. http://www.cafesoft.com/products/cams/ps/docs30/admin/ConfiguringApache2ForSSLTLSMutualAuthentication.html
PS: the man behind X509 auth code in web2py is mcm, sadly for your it's documented how it works but not how to organize the certs (which in theory you should know in advance) --

