This is a good and involved question. There are pros and cons to both models. The main advantage to one large database is that you can analyze (search, mapreduce, etc) across all users very easily. The main advantage of one-db-per-user is that every user has their own data "sandbox", which may be nice for your SLA. Additionally, that means that the amount of data in each user database can be relatively small.
If you can provide more details about the data you are storing, the relational modeling, and the queries you hope to be able to do, I can probably give you a more satisfying answer.