(My solution to your problem is at the end of this post)
I have got a sony vaio Z790 laptop, with an onboard Intel graphics card an a dedicated GeForce 9300M gs Nvidia card. I am working on Ubuntu Oneiric 11.10.
When using windows I can only switch between them using a hardware switch, so I assume that my model does not support the Nvidia "Optimus" technology.
I still haven't managed to work with the Nvidia card and I am stuck with the integrated from intel. When I install the Nvidia drivers (either from their website or using jockey) and restart X, I get a black screen. I have fiddled a bit with the xorg.cong file (adding various options such as a custom monitor EDID (CustomEDID option), specifying explicitly where the Nvidia card is connected (using the BusID option) and others, but the furthest I have got is to get a small white window on the top left of a totally black screen.
Back to your problem: From what I have experienced, my understanding is that once you install an nvidia driver your whole OpenGL configuration is messed-up. Even if you uninstall the drivers afterwards using nvidia-uninstall, still you wont get the 3D unity interface when you restart.
I have written the following little script which combines things I have read in varius forums, which always restores the intel configuration after an unsuccessful attempt to install some kind of driver to get my nVidia card working:
(note the this might mess-up your bumblebee configuration - I haven't looked a lot into bumblebee yet)
sudo apt-get purge nvidia*
sudo apt-get install --reinstall xserver-xorg-video-intel libgl1-mesa-glx:amd64 libgl1-mesa-glx:i386 libgl1-mesa-dri:amd64 libgl1-mesa-dri:i386 xserver-xorg-core
sudo dpkg-reconfigure xserver-xorg
sudo update-alternatives --remove gl_conf /usr/lib/nvidia-current/ld.so.conf
sudo rm /etc/X11/xorg.conf
sudo stop lightdm
sudo start lightdm
Instead of typing the commands one by one, you can
1. copy this script to a new file
2. save it as you wish (e.g. "fix.run")
3. open a terminal, navigate to the directory where your script is
4. execute the command "sh fix.run" (replace fix.run with your filename)
(Note that I have no idea if the last 2 commands will work in earlier versions of ubuntu - I am new to linux. In case they don't, just find out how to restart your X server, or try hitting ctrl+alt+backspace or ctrl+print screen+k).
Hopefully you will fall back on your intel configuration with the nouveau drivers and after a few seconds you will be back on unity 3D.
Hope this helps,