This should be a simple thing. But from what I can tell NVidia's TwinView driver doesn't support different monitor rotations (under Linux). But having X Windows it should still be easy using dual X Screens. It should just be a matter of going to NVidia X Server Settings, selecting "Separate X Screen" and then selecting "Enable Xinerama". Unfortunately for me, this caused general weirdness where the first screen was mostly black and the second screen was displayed horizontally.
The way I fixed the problem was to disable Compiz. The easiest way I found to disable Compiz was to log in using the "Ubuntu Classic (No effects)" session.
Then it was just a matter of enabling multiple XServers and Xinerama and enabling rotation (RandRRotation). Here are the bits in my xorg.conf to rotate my second monitor to the left:
Section "Monitor" # HorizSync source: edid, VertRefresh source: edid Identifier "Monitor1" VendorName "Unknown" ModelName "DELL U2711" HorizSync 29.0 - 113.0 VertRefresh 49.0 - 86.0 Option "RandRRotation" "on" Option "DPMS" EndSection
Section "Screen" Identifier "Screen1" Device "Device1" Monitor "Monitor1" DefaultDepth 24 Option "TwinView" "0" Option "metamodes" "DFP-2: nvidia-auto-select +0+0" Option "Rotate" "left" SubSection "Display" Depth 24 EndSubSection EndSection