I haven't used authoxy on Panther; several months ago I switched to squid to "proxy my proxy" and never looked back. The big advantage squid had then was handling https sites, though authoxy eventually handled this (maybe when it became shareware?).
Cutting to the chase:
(1) proxy support in Panther is better, but far from ideal. For example, software update works fine, but iTunes doesn't handle proxies well. (In case it's not clear from the context, I'm talking about authenticating proxy servers here, which is the usual situation in which something like authoxy is required).
(2) have a look at squidman if you decide that the native proxy support isn't cutting the mustard. It provides a nice GUI front end to a squid proxy server. Some complain about massive overkill in using squid for this purpose, but it's worked really well for me. The only hiccough being an occasional need to HUP the squid daemon. (You can doubtless do this through the GUI as well.) This might happen once a month or so. Squidman is available (freeware) on versiontracker. You can set it as a login item so that *squidman* quits after launch, leaving your squid server active. Most helpful.
Just configure the "Parent" tab with the details of your authenticating proxy server, and use 127.0.0.1 together with the squid port (default is 3128) in your proxy settings within the Network Preferences Panel.
Cheers,
Paul