I've had a Logitech MX1000 mouse for a few years now, and the two most important features for me have been the ergonomic build and the few extra buttons. Something I've always found with many-buttoned mice is that the side button closest to the thumb is a much more ergonomic way to "middle click" than the actual middle mouse button---it's a much more natural motion. Middle clicks are quite useful these days, especially with them being a standard way of closing tabs (and opening them in browsers), and having such a popular button perched on a rocking and rolling peak is far from ideal.

Since I'm primarily a Linux user, I don't have Logitech's own SetPoint software at my disposal, so I've always had to find a way to get this functionality in some other way. When I first got the mouse, this method involved deliberately using a "basic" mouse driver (referred to in xorg.conf as "IMPS/2"), which didn't support many mouse buttons. The effect was that the button mappings wrapped around, leaving button 8, my preferred "middle click", mapped to button 2 (8 mod 3), the real middle button.

Unfortunately, newer Xorg versions became smarter and better capable of handling more buttons, and this workaround ceased to function. For the next while, I used something even more hackish: xbindkeys combined with xmacroplay to simulate a middle click with the following part of my .xbindkeysrc:

"echo ButtonRelease 8 ButtonPress 2 ButtonRelease 2 | xmacroplay -d 0 :0.0 &"
    b:8

The downside to this solution is that there are some cases where the button events don't work correctly, one of them being open-in-tab from a bookmark menu in Firefox. It seemed the best solution would be to get Xorg to remap the buttons in such a way that button 8 really was just an extra button 2. The "xinput" utility lets you set button maps in this way---this wiki entry shows how to remap mouse buttons (even if for a different purpose).

This method worked fine, and I put it in my startup programs for GNOME, but it didn't persist after suspend/resume. It appears that when resuming, USB devices get "reattached", and therefore don't keep the settings applied to them the last time they were attached. The workaround for this is to set a policy using a HAL (Hardware Abstraction Layer) .fdi file. These files live in /etc/hal/fdi/policy (at least they do on Ubuntu) and allow you to set various properties on input devices. This page on the Ubuntu wiki gave me the recipe I needed to remap buttons based on the device name. I ended up with the following .fdi file (which I saved at /etc/hal/fdi/policy/logitech-mx1000.fdi):

<deviceinfo version="0.2">

<!-- Remap Logitech MX1000 buttons so that the most accessible side button
     acts as a middle button -->

  <device>
    <match key="info.product" string="Logitech USB RECEIVER">
      <merge key="input.x11_options.ButtonMapping" type="string">1 2 3 4 5 6 7 2</merge>
    </match>
  </device>

</deviceinfo>

Now, whenever my Logitech mouse is connected, it gets the buttons remapped---this includes when resuming from suspend. Problem solved... until things are changed again of course!