If by "two web2py apps" you mean two different web2py installations (with 
the web2py code duplicated, so that they can run different versions of 
web2py, for example), then I can say: we recently followed this tutorial:

http://www.techshinobi.com/index.php/multiple-web2py-instances-with-uwsgi-emperor-and-nginx/

and it worked for us.

If your two web2py apps can share the web2py code, and you can arrange the 
routing staff to your satisfaction, you don't even need that.

Have you tried to just define several sites in /etc/nginx/sites-available, 
one of them as in the web2py book, two of them like in the default nginx 
site? Then: what error do you get, can you post your conf files, etcetera?

-- 
Resources:
- http://web2py.com
- http://web2py.com/book (Documentation)
- http://github.com/web2py/web2py (Source code)
- https://code.google.com/p/web2py/issues/list (Report Issues)
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