For what it's worth, I'm not from GPSoft and these forums are for user-to-user discussion, rather than an official support channel. That said, the GPSoft guys also read and post here (time permitting) and we've got a good community of helpful people here who you can depend on to help.
If you do need the official support channel it's at gpsoft.com.au/Support.html but, with this kind of open-ended question, I'd say you've come to the right place since there may be other people reading the forum who have experienced something similar and have suggestions.
To keep things simple, please try to avoid opening that directory until we get to a stage where an empty directory is working. I say this because there may be more than one problem and that could really confuse things. For example, sometimes either viewer plugins or shell extensions crash when they encounter certain files. In a directory with a lot of files, and many different types of files, there's a chance that one of the files is causing a crash which isn't related to the other problem.
There's a FAQ which guides you through working out if certain files or types of files are causing a crash and what to do if they are but I would say we're better off leaving that potential issue for now and concentrating on the more simple case of an empty directory. Once that works we can see if the big directory works.
There could be a problem in the registry, or something interfering with DDE or a similar launch system, which is causing the problem with all three programs (Opus, Thunderbird and GAIM). At least, if you meant that you were clicking on HTTP:// links in the other two programs. (For what it's worth, I ran Thunderbird and Opus side-by-side for a long time without any conflicts.)
If you go to Start->Run, type google.com and then hit return, does that work okay?
It's possible that anti-spyware/virus software is blocking programs from launching URLs and folders. You said you tried disabling those tools but, at least if we get stuck, it may be worth a try completely removing them. I don't know about these particular tools but I know that others (e.g. ZoneAlarm) can cause problems even when disabled, while unisntalling them can make the issues go away. Not guaranteed but worth a try, especially if reinstalling them isn't a hassle.
From what you describe, it looks like the Desktop menu works okay while opening from the tray icon or shortcuts doesn't work:
Working:
[ul][li]Desktop double-click (in empty space).[/li]
[li]Desktop context menu, New Lister.[/li]
[li]Desktop context menu, Preferences.[/li][/ul]
Not working:
[ul][li]Tray icon double-click.[/li]
[li]Tray icon menu, Preferences.[/li]
[li]Desktop shortcuts.[/li][/ul]
Could you open Preferences and go to Double-Click - Desktop, then confirm that the Desktop and Tray Icon settings do the same thing? If they are identical, could you quickly do a sanity check and first open the lister using the method which works (Desktop double-click), then close it and try the method which doesn't work (Tray icon double-click).
Between doing the two tests, please ensure you don't change directories or anything. Just open a lister, close it, then try to open it via the other method.
If both methods are configured to do exactly the same thing and one method works but then other immediately fails then we can rule several things out as the issue must be down to the mechanisms, rather than what is being triggered by them.