Just a couple I've spotted so far:
Windows keep preference settings when you open them via the Finder, however if opened from the Dock, they revert to column view. It may be because I've set my prefs to open all new windows as column view, but that shouldn't make any difference as they're not new windows! For example, make sure you've got no windows open and use the Go menu to get the Applications folder. Set it to icon view (got mine set to stay sorted by name as well). Close the window and reopen it from the Go menu just to make sure your prefs have stuck. Now open Applications from the Dock - BAM, column view. That's happened on two different machines that have both had "erase and install" done on them.
Safari doesn't recognise some security certificates that it used to. IE is still fine with them.
Can't get browse Appletalk notwork to work (might be our daft notwork at the office though)
I'm sure the list will grow .....