Question: I'm trying to put the finishing bits and pieces on a client / server application I'm writing, but something seems to go foul at the last step in the SSL handshake.

The client side of the program connects and establishes a secure connection with a server without a hitch, but if I want to run operations from the server side of the program, it fails to make any connection. 

When I try to connect to my server via Firefox (as the client), the browser will alert to me that the certificate is not suitable for the connection.

On the server side, my logs reflect that there's an `unknown ca` or `certificate unkown` whenever I try to accept bytes from my client.

I guess my question boils down to this point:

Do you have to make different certificates for a client side application vs a server side application? What's the difference between these?

Answer: 
The same way that server certificates uniquely identify a server (or domain), client certificates uniquely identify a client. And just like server certificates must be signed by someone the client trusts, client certificates must be signed by someone the server trusts.

Usually, when you configure a server to accept client certificates, you specify a signing certificate that must be used to sign the client's cert. This lets the server know that the client is "authorized", whatever that might mean in your context, since presumably you'll only sign certificates for "authorized" users.

Allowing client certificates without doing any sort of verification is generally possible with most servers, but sort of defeats the whole purpose.
*jtpresta* in one of his comments indirectly makes an interesting but very true point: SSL client authentication is a mess. It's good because it's absolutely secure, but it's crappy because it's difficult both to set up and to maintain. 

Unless you have a really good reason, go with shared-key authentication instead (i.e. "password"). You'll save time and money. SSL authentication is good for when security trumps cost by a fairly wide margin.