I work from a variety of computers, and to keep my notes centralised and privately accessible wherever I am, I use putty as a socks5 server to login to my home (ubuntu) pc that serves local (behind a router) web pages. I can tell Firefox to use the socks5 connection, but there are two problems:

1. This directs all Firefox traffic through the proxy
2. I don't normally use Firefox

Is there a way, on a system wide level, to redirect specific traffic through my ssh/socks proxy?

Why not just port tunnel the port you want to your home connection through putty, no need to use a proxy server within firefox, etc. Unless you're trying to accomplish something differently.

That can be messy: putting putty in your socks. Squelches when you walk.

Ah, putty is more featureful than I realised. I had a dynamic tunnel set up for port 9000, which I used with Firefox's socks proxy configuration. I did more reading and found the better way. I didn't understand "destination" is relative to the remote machine, so localhost is the remote machine. Source port is what you connect to, so in my case, I put localhost:9999 iuto my browser, and get to 192.168.1.2:80 on the remote machine.

This link is really helpful:
http://www.securityfocus.com/infocus/1816

I can even remote desktop to my work pc from home, after remote port forwarding port 3389!

Thought I'd give an update.. Found what I was really looking for with Privoxy. Putty still opens a socks connection to my home server, but Privoxy routes all system network traffic (based on some simple pattern matching) through it. So, doesn't matter that Opera and Chrome don't have native socks support, and I can decide which traffic goes where. As an added bonus, Privoxy comes with sweet ad filters out of the box.