I found a good answer in the comments in this link:
http://blog.boxedice.com/2010/02/28/notes-from-a-production-mongodb-deployment/
Basically option #2 seems to be the best way to go.
Quote from David Mytton's comment:
We decided not to have a database per
customer because of the way MongoDB
allocates its data files. Each
database uses it’s own set of files:
The first file for a database is
dbname.0, then dbname.1, etc. dbname.0
will be 64MB, dbname.1 128MB, etc., up
to 2GB. Once the files reach 2GB in
size, each successive file is also
2GB.
Thus if the last datafile present is
say, 1GB, that file might be 90% empty
if it was recently reached.
from the manual.
As users sign up to the trial and give
things a go, we’d get more and more
databases that were at least 2GB in
size, even if the whole of the data
file wasn’t use. We found this used a
massive amount of disk space compared
to having several databases for all
customers where the disk space can be
used to maximum efficiency.
Sharding will be on a per collection
basis as standard which presents a
problem where the collection never
reaches the minimum size to start
sharding, as is the case for quite a
few of ours (e.g. collections just
storing user login details). However,
we have requested that this will also
be able to be done on a per database
level. See
http://jira.mongodb.org/browse/SHARDING-41
There are no performance tradeoffs
using lots of collections. See
http://www.mongodb.org/display/DOCS/Using+a+Large+Number+of+Collections