By "properly" you mean that the Useragent sent to the web server would be different than that seen by Java. Yes that would solve bug 83376 but I believe that actually separating the two (the only way of solving 83376) is a necessary first step to implement useragent per-site setting, which is a much bigger task. This means that bug 83376 is actually a proxy for "Separate the useragent used by http from the real one seen by plug-ins". This is while confirming this bug I mark it as dependant on bug 83376. If we create a new useragent separation bug, the depandance should be moved.
Okay, I've created bug 102042 to look into the "splitting" problem like you suggested. (I used your wording for the summary; hope that's okay.) While this one does seem a bit daunting, I'm willing to look into bug 102042, though I don't actually have any experience with coding Mozilla, so if someone with more experience than I is interested, you'd be able to code it much faster than I could.
Trying to change the preferences back end to support multiple entries for a preference would be essentially a total re-write. There is a preference out there "network.proxy.no_proxies_on" which is used in the manner you suggest. The code which uses it saves the list out as one long string preference and parses it when it is loaded. You might consider a solution like this. mtoltz and I have also talked about this general principle a couple of times as he has also expressed an interest in per site preferences for security. Adding him to the cc list because I know he has given this some thought.
Replacing fields that bugzilla removed/changed with my last comment.
Believe this is what bug 80658 talks about doing, marking as a dup. *** This bug has been marked as a duplicate of 80658 ***
mass verification of duplicate bugs: to find all bugspam pertaining to this, set your search string to "DuplicateBugsBelongInZahadum". if you think this particular bug is *not* a duplicate, please provide a compelling reason, as well as check a recent *trunk* build (on the appropriate platform[s]), before reopening.