I've written a post on Sourcing's blog about structuring Sinatra apps.
I love Sinatra. I use it for practically everything. For me, Sinatra has the perfect blend of simplicity and abstraction. I can understand the full stack, dip into the source when I need to, and extend the framework how I see fit.
However the bare-bones nature of Sinatra can come at a cost. Sinatra leaves much more of the decision making around your application's structure, layout and libraries up to you. This can be a bit daunting if you're just getting into Ruby web app development, which I think is one of the reasons why Sinatra is mainly the realm of more experienced developers looking for a bloat-free alternative to Rails.