My site has an SSL certificate from a certified authority.
I have Piwik setup on a server in our office, and pull the tracking code from it on each page view.
I realise that Piwik's javascript needs to be served over SSL if I want to avoid "untrusted content" browser warnings.
Can I use a self-signed certificate for this? Will browsers pick up on the fact that our site embeds code from another site that uses a self-signed certificate?
No, you can't use a self-signed certificate for embedded code. If you do this the browser will either complain or silently not load the insecure content (insecure because the identity could not be verified).