An updated version of my suggestion (should be more intuitive)

[Yuan Qi <gmanenews 3 maxchee spamgourmet com>]

Ubuntu Bugzilla Entry: https://bugzilla.ubuntu.com/show_bug.cgi?id=9125

Ubuntu Hoary Nautilus Bug: https://bugzilla.ubuntu.com/show_bug.cgi?id=8516

Here is the new version of the suggestion:

A folder will automatically roll-up when the user opens one of its
subfolders for the first time.

If the *very next* action performed by the user *on the autorolled
folder* is to bring it up again, then a flag will be set to tell 
nautilus not to autoroll it the next time.

That folder will not roll-up automatically the next time the user opens 
a subfolder from it.

If the *very next* action performed by the user on that particular 
parent window this time is to roll it up (or minimized it), then the 
flag will be deleted and the folder will be autorolled the next time.

This suggestion, however, will not solve the cluttering on the taskbar.