In terms of general UI, navigation on the left is more functional. I really hated Microsoft for putting the scroll bar on the right side. In Nextstep, the scroll bar was on the left side and it was much easier to navigate from the left. I've used both, and left side navigation was definitely easier.
In terms of navigation, the pull down menus are all on the left (File, Edit, View, Favorites, etc). So getting from the pulldown menu to the scroll bar or sidebar would be less distance if the scrollbar and the sidebar was on the left.
When I am programming or composing a document, my cursor was more often on the left side of the editor than the right side and so it was faster for me to move from the cursor to the scrollbar (or sidebar) if it was on the left.
http://www120.pair.com/mccarthy/nextstep/intro.htmld/
"NEXTSTEP scrollbars haven't changed in 10 years, and there is still no reason for them to do so, since they were "just done right" the first time. (This is a recurring theme with NEXTSTEP, you will find.) First, the (vertical) scrollbar is on the left. Because the menu appears on the left, this saves the user time going between the two. (The scrollbars really should be on the left in the MacOS and Windows, too, considering that the most often used menu items are also towards the left.) The fact that most text in any given document will be on the left of the window is yet another reason for the scrollbar to be on the left, since that is the side of the window the cursor is most likely to be during editing. In addition, the left-side scrollbars mean that a window can be fully functional when part of it is off-screen to the right. Send the right side of a window off-screen in MacOS or Windows, and while you can get to the menus and buttons, you won't be able to scroll."
http://lucy.ifi.unibas.ch/Groups/Sta...scrollers.html
"Why have the scrollbar on the left?" -Imagine you don't have a scroll button on your mouse like in the past.
The last link really shows why having the navigation on the right sucks. In that exaggerated example, you can't possibly read the text and grab the scroll bar at the same time.
So, while I prefer left side navigation/sidebar etc over the right side, I would prefer it not to be there at all if it isn't required. In our case, a couple of the items are useful (search, profile, etc) so put those at the top and get rid of the sidebar altogether. That should make everyone happy.