When I try to run app.py (Python 3.3, PyCrypto 2.6) my virtualenv keeps returning the error listed above. My import statement is just from Crypto.Cipher import AES
I've had the same problem 'ImportError: No module named Crypto.Cipher', since using GoogleAppEngineLauncher (version > 1.8.X) with GAE Boilerplate on OSX 10.8.5 (Mountain Lion). In Google App Engine SDK with python 2.7 runtime, pyCrypto 2.6 is the suggested version.
The solution that worked for me was...
1) Download pycrypto2.6 source extract it somewhere(~/Downloads/pycrypto26)
e.g., git clone https://github.com/dlitz/pycrypto.git
2) cd (cd ~/Downloads/pycrypto26) then
3) Execute the following terminal command inside the previous folder in order to install pyCrypto 2.6 manually in GAE folder.
sudo python setup.py install --install-lib /Applications/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine