I might be smokin’ crack, but I think that todays (September 30th, 2008) Java update from Apple finally fixed the command-tab issue. I haven’t verified it with different apps yet, but the ones I use regularly seem to be working as expected when you command-tab to them.
Found a good shortcut for getting access to hidden folders in OS X file dialogs and the Finder. It requires some typing and it doesn’t auto-complete like Linux does, but it is better than nothing. Just hit Shift-Command-G to open the “Go To Folder” dialog and then type the path to the hidden file or folder. The path can be relative.
Now, just need to figure out how to access hidden files from the Finder and file dialogs.
[Edit 08/09/2008] The issue is that using the AppleShowAllFiles configuration doesn’t work in dialog boxes and if you enable it, opening Finder in your home directory gets REALLY messy. What Apple needs is the same feature that Linux has had for a long time: the ability to show and hide hidden files in dialogs and finder using a keyboard shortcut or menu option. I believe Linux uses ctrl-h for this. Apple could use something like cmd-shift-h or something.