Here is what I did:

1. You can use xscreensaver-command -watch to monitor xscreensaver events, so you can actually run a program when xscreensaver is activated (for example, to disable compiz-fusion), and another one when it is deactivated (to bring compiz-fusion back). I modified the following script available from the xscreensaver man pages and saved it as ~/bin/fixscreensaver:

   #!/usr/bin/perl
   
   # Fixes xscreensaver when compiz is running
   
   my $blanked = 0;
   open (IN, "xscreensaver-command -watch |");
   while () {
     if (m/^(BLANK|LOCK)/) {
       if (!$blanked) {
         system "usemetacity";
         $blanked = 1;
       }
     } elsif (m/^UNBLANK/) {
       system "usecompiz";
       $blanked = 0;
     }
   }

2. As you can see, the script above calls usemetacity when xscreensaver is activated and usecompiz when it is deactivated. Save the following script as ~/bin/usemetacity:

   #!/bin/bash
   
   #killall gkrellm
   metacity --replace &
   #sleep 1
   #gkrellm &

3. Now save this one as ~/bin/usecompiz:

   #!/bin/bash
   
   #killall gkrellm
   compiz --replace &
   #sleep 2
   #gkrellm &
   #windowranger

4. Add ~/bin/fixscreensaver to the list of startup applications (System > Preferences > Sessions > Startup programs) and also make sure that ~/bin/ is in your $PATH environment variable.
5. Optional: If you use gkrellm, you should uncomment the corresponding lines in the scripts above. Those lines will prevent metacity (the default gnome window manager) and compiz-fusion from changing the position of the gkrellm window, which happens everytime you switch between the two because these window managers use different ways to describe desktop geometry.
6. Optional: You can also use the usecompiz and usemetacity scripts to manage any other application that misbehaves when metacity or compiz-fusion take over your desktop. In fact, I use the windowranger script below to automatically put windows back into their corresponding viewports since everything gets shoved into the first viewport once you go back into compiz from metacity (thanks for pointing it out darken). You will need wmctrl for this to work properly:

   #!/usr/bin/python
   
   import os, time, wnck, sys
   
   def dec2hex(n):
     #"""return the hexadecimal string representation of integer n"""#
     return "%X" % n
   
   def hex2dec(s):
     #"""return the integer value of a hexadecimal string s"""#
     return int(s, 16)
   
   def MoveWindow(wID, wtitle, xpos, ypos):
   
       time.sleep(0.2)
       os.system('wmctrl -i -r ' + wID + ' -e 0,'+str(xpos)+','+str(ypos)+',-1,-1')
       #time.sleep(0.4)
       #os.system('wmctrl -i -a ' + wID)
       if DEBUG: print "Moved to", xpos, ypos, 'n'
   
   def Place(x, y, wID, wclass, wtitle):
   
     fin,dout = os.popen4('wmctrl -d')   # output desktop geometry
     for line in dout:
       line = line[line.find('VP: ') + 4:len(line)]  # get current viewport offset
       line = line[0:line.find(' ')]
       offset = line.split(',')      # split in x,y viewport offset coordinates
       vpxpos = int(offset[0])       # convert into integer
       vpypos = int(offset[1])       # convert into integer
       absxpos = vpxpos+x            # absolute window position (x)
       absypos = vpypos+y            # absolute window position (y)
       wxpos = absxpos
       wypos = absypos
       while wxpos >= width:
         wxpos = wxpos - width       # relative window position (x)
       while wypos >= height:
         wypos = wypos - height      # relative window position (y)
       if (wxpos >= 0)&(wxpos <= 2): wxpos = 0
       if (wypos >= 0)&(wypos <= 2): wypos = 0
   
     dout.close()                    # close command output
     if DEBUG: print 'Position:', absxpos, 'x', absypos
   
     #Send Firefox to viewport 1
     if wclass.find('Firefox') != -1:
       # Flash fullscreen windows are titled 'Firefox' so we need to ignore them...
       if wtitle != 'Firefox':
         MoveWindow(wID, wtitle, wxpos - vpxpos + vpx1, wypos - vpypos + vpy1)
   
     #Send GYachI to viewport 2
     elif wclass.find('GYachI') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx2, wypos - vpypos + vpy2)
   
     #Send VirtualBox to viewport 5
     elif wclass.find('VirtualBox') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx5, wypos - vpypos + vpy5)
   
     #Send Amarok to viewport 6
     elif wclass.find('Amarokapp') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx6, wypos - vpypos + vpy6)
   
     #Send Azureus to viewport 6
     elif wclass.find('SWT') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx6, wypos - vpypos + vpy6)
   
     #Send Qbittorrent to viewport 6
     elif wclass.find('Qbittorrent') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx6, wypos - vpypos + vpy6)
   
     #Send Pidgin to viewport 7
     elif wclass.find('Pidgin') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx7, wypos - vpypos + vpy7)
   
     #Send Skype to viewport 7
     elif wclass.find('Skype') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx7, wypos - vpypos + vpy7)
   
     #Send Thunderbird to viewport 8
     elif wclass.find('Thunderbird-bin') != -1:
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx8, wypos - vpypos + vpy8)
   
     #Send all other windows in viewport 1 to viewport 2
     elif (wclass.find('Gnome-panel')==-1)&(wtitle != 'Desktop')&(wclass.find('Gkrellm')==-1)&(wclass.find('Launcher')==-1)&(absxpos < width)&(absypos <= height):
       MoveWindow(wID, wtitle, wxpos - vpxpos + vpx2, wypos - vpypos + vpy2)
   
     else:
       if DEBUG: print 'Ignoredn'
   
   #---------------------------- MAIN -------------------------------------
   s = wnck.screen_get_default()
   width = s.get_width()
   height = s.get_height()
   vpx1 = (width * 0);vpy1 = (height * 0)
   vpx2 = (width * 1);vpy2 = (height * 0)
   vpx3 = (width * 2);vpy3 = (height * 0)
   vpx4 = (width * 3);vpy4 = (height * 0)
   vpx5 = (width * 0);vpy5 = (height * 1)
   vpx6 = (width * 1);vpy6 = (height * 1)
   vpx7 = (width * 2);vpy7 = (height * 1)
   vpx8 = (width * 3);vpy8 = (height * 1)
   DEBUG = False;
   
   for arg in sys.argv:
     if arg=='--debug':
       DEBUG=True;
   
   if DEBUG: print 'Viewport geometry:', width, 'x', height, 'n'
   
   fin,wout = os.popen4('wmctrl -lGx')
   for line in wout:
     wID = line[0:line.find(' ')]                      # get the window ID
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wdesk = line[0:line.find(' ')]                    # get the window desktop
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wxoffset = line[0:line.find(' ')]                 # get the window x offset
     wxoffset = (int(wxoffset) / 2)
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wyoffset = line[0:line.find(' ')]                 # get the window y offset
     wyoffset = (int(wyoffset) / 2) - 24
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wwidth = line[0:line.find(' ')]                   # get the window width
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wheight = line[0:line.find(' ')]                  # get the window height
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wclass = line[0:line.find(' jsilva')]             # get the window class
     line = line[line.find(' jsilva'):len(line)]
     line = line.lstrip()
     whost = line[0:line.find(' ')]                    # get the window host
     line = line[line.find(' '):len(line)]
     line = line.lstrip()
     wtitle = line[0:len(line) - 1]                    # get the window title
     if DEBUG:
       print 'Class:', wclass
       print 'Host:', whost
       print 'Title:', wtitle
     Place(wxoffset,wyoffset,wID,wclass,wtitle)  # place window
   wout.close()

7. Enjoy!