Support for proxy autoconfiguration on Windows seems so "seamless" because it's implemented by the WinHTTP client, which is stored in a DLL accessible to all applications with a public API. Many applications use WinHTTP and get proxy-autoconfiguration "for free".
In the Linux world, each application is typically making its own socket calls and using its own implementation of the HTTP protocol. There are HTTP libraries out there, but it's much more likely, as compared to Windows, that applications are going to handle doing HTTP on their own and probably won't have a Javascript interpreter necessary to process a proxy autoconfiguration file.
You might consider running a local proxy server on the Linux machine, specifying itself as the HTTP_PROXY system-wide, and then configuring that local proxy server with the necessary rules to access some sites directly versus using the corporate proxy as a parent.
Squid could do what you want, but it's fairly heavyweight. I just found this interesting tinyproxy project, and it certainly looks promising (allows for selective use of an upstream proxy by domain, very lightweight, etc), but I've never used it personally and know nothing about it. (In theory, one could modify tinyproxy to actually parse the proxy autoconfiguration file. That'd be a really neat trick, though not something I have time to work on...)
Squid is only a HTTP proxy. Are you sure you want the traffic to pass through the PC, or do you just want to monitor all traffic on the network? Passing through the PC is a lot harder with only 1 interface card. Unfortunately, a lot of these tools are somewhat complex to use, because, well, it is a complex thing you're trying to do. Wireshark will definitely be able to monitor all traffic on the network. Proxying, unfortunately, for all sorts of traffic (not just HTTP) is a lot harder.
Best Answer
Squid is the standard proxy solution for Linux systems, and it's usually the best one.
You can disable logging, filtering, caching and rewriting by appropriately editing
squid.conf, and the resulting system will be very small and fast (although even a little bit of caching usually helps a lot).I think you should tinker with it a little more and try to configure it for your needs; Squid really is one of the best proxies around, and I don't see any better solution on Linux.