Pretty much like Michael, I've been battling the obtuseness of the Firefox and Thunderbird ports to Mac OS X. Since (due to Apple's own set of dumb limitations regarding the systemwide SOCKS settings) I'm using them to replace Safari and Mail.app while on vacation, I've been caught out more than once where it relates to key bindings and plain usability, since none of them follows Mac OS X standard practice to any great degree.
Both of them are, at first sight, good-looking and intuitive applications which have been adapted to Mac OS X with far better taste than most ports. But after using them for a while, their un-Macness starts creeping up on you. I pretty much live inside Firefox on Windows and rely exclusively on Thunderbird for my UNIX mail, but, like Michael, I find it odd that they behave strangely on Macs.
My main gripes are with Thunderbird, actually - its new "offline" mode badly needs more user feedback and UI features, since it is all too easy to completely botch it up. For one, when going offline for the first time, you are not prompted to mark folders for offline use - and, most seriously of all, non-default accounts' inboxes do not seem to be included by default.
There is also no way to trigger the offline/sync process via a nice, fat toolbar button or a hotkey - you only get the shrivelled little connection widget on the bottom left-hand side of the window, an obscure sub menu, and a progress bar that vanishes at the slightest provocation (and this last one is not Mac OS X-specific, I find the lack of decent status bar feedback annoying on Linux and Windows as well).
The "stop transfers" button also seems pretty useless, since it too does not update the status bar (and I'm not certain it actually does anything sometimes).
Finally, there is no indication on the message list that a message has been successfully downloaded, is available offline, or has been changed (flagged, moved, read, etc.) in offline mode. Just changing the message color (dimming or tinting the text) would suffice, but no, there is nothing.
And the status bar just sits there, failing to provide any useful information.
The upshot of this bad interaction design is that it becomes a major nuisance to figure out what is happening/will happen when you either enter or leave offline mode. The application behaviour is unpredictable, unfathomable, and leaves your users in a state of unrest (or outright distrust towards your application), which, as you may have gathered from years of indoctrination from such industrious luminaries as Tog, is, in a word, bad.
Couple that with lack of standard keybindings, odd-looking widgets and wierd font defaults and, no matter how polished the UI, you have a poor Mac OS X citizen (despite kickass application icons).
Mozilla zealots will likely point out that there is copious documentation on the net, that the offline feature is a recent extension, and that the keybindings make perfect sense across platforms - all of which is hogwash. If you design anything to run across several platforms, success is still measured on a platform-by-platform basis. And it will only succeed on each individual platform if you adopt its individual UI dialect and interaction patterns.
Given the time and effort that obviously went into the Mac OS X ports, someone at the Mozilla team certainly understands some of this. But they fell short of full native behavious, and on the Mac's streamlined interface, any variations (like different keybindings and widgets) stick out like a sore thumb - and need to be fixed.
Oh, and for chrissakes, somebody tell me how to get rid of the attachment listing inside the preview pane - it`s a waste of screen real estate, and it belongs next to the mail headers.