Here is a basic template for Sinatra apps that I use. (My larger apps have 200+ files broken out like this, not counting vendor’d gems, covering 75-100 explicit routes. Some of these routes are Regexp routes covering an additional 50+ route patterns.) When using Thin, you run an app like this using:
thin -R config.ru start

Edit: I’m now maintaining my own Monk skeleton based on the below called Riblits. To use it to copy my template as the basis for your own projects:

# Before creating your project
monk add riblits git://github.com/Phrogz/riblits.git

# Inside your empty project directory
monk init -s riblits

File Layout:

config.ru
app.rb
helpers/
  init.rb
  partials.rb
models/
  init.rb
  user.rb
routes/
  init.rb
  login.rb
  main.rb
views/
  layout.haml
  login.haml
  main.haml

 
config.ru

root = ::File.dirname(__FILE__)
require ::File.join( root, 'app' )
run MyApp.new

 
app.rb

# encoding: utf-8
require 'sinatra'
require 'haml'

class MyApp < Sinatra::Application
  enable :sessions

  configure :production do
    set :haml, { :ugly=>true }
    set :clean_trace, true
  end

  configure :development do
    # ...
  end

  helpers do
    include Rack::Utils
    alias_method :h, :escape_html
  end
end

require_relative 'models/init'
require_relative 'helpers/init'
require_relative 'routes/init'

 
helpers/init.rb

# encoding: utf-8
require_relative 'partials'
MyApp.helpers PartialPartials

require_relative 'nicebytes'
MyApp.helpers NiceBytes

 
helpers/partials.rb

# encoding: utf-8
module PartialPartials
  def spoof_request(uri,env_modifications={})
    call(env.merge("PATH_INFO" => uri).merge(env_modifications)).last.join
  end

  def partial( page, variables={} )
    haml page, {layout:false}, variables
  end
end

 
helpers/nicebytes.rb

# encoding: utf-8
module NiceBytes
  K = 2.0**10
  M = 2.0**20
  G = 2.0**30
  T = 2.0**40
  def nice_bytes( bytes, max_digits=3 )
    value, suffix, precision = case bytes
      when 0...K
        [ bytes, 'B', 0 ]
      else
        value, suffix = case bytes
          when K...M then [ bytes / K, 'kiB' ]
          when M...G then [ bytes / M, 'MiB' ]
          when G...T then [ bytes / G, 'GiB' ]
          else            [ bytes / T, 'TiB' ]
        end
        used_digits = case value
          when   0...10   then 1
          when  10...100  then 2
          when 100...1000 then 3
          else 4
        end
        leftover_digits = max_digits - used_digits
        [ value, suffix, leftover_digits > 0 ? leftover_digits : 0 ]
    end
    "%.#{precision}f#{suffix}" % value
  end
  module_function :nice_bytes  # Allow NiceBytes.nice_bytes outside of Sinatra
end

 
models/init.rb

# encoding: utf-8
require 'sequel'
DB = Sequel.postgres 'dbname', user:'bduser', password:'dbpass', host:'localhost'
DB << "SET CLIENT_ENCODING TO 'UTF8';"

require_relative 'users'

 
models/user.rb

# encoding: utf-8
class User < Sequel::Model
  # ...
end

 
routes/init.rb

# encoding: utf-8
require_relative 'login'
require_relative 'main'

 
routes/login.rb

# encoding: utf-8
class MyApp < Sinatra::Application
  get "/login" do
    @title  = "Login"
    haml :login
  end

  post "/login" do
    # Define your own check_login
    if user = check_login
      session[ :user ] = user.pk
      redirect "https://stackoverflow.com/"
    else
      redirect '/login'
    end
  end

  get "/logout" do
    session[:user] = session[:pass] = nil
    redirect "https://stackoverflow.com/"
  end
end

 
routes/main.rb

# encoding: utf-8
class MyApp < Sinatra::Application
  get "https://stackoverflow.com/" do
    @title = "Welcome to MyApp"        
    haml :main
  end
end

 
views/layout.haml

!!! XML
!!! 1.1
%html(xmlns="http://www.w3.org/1999/xhtml")
  %head
    %title= @title
    %link(rel="icon" type="image/png" href="https://stackoverflow.com/favicon.png")
    %meta(http-equiv="X-UA-Compatible" content="IE=8")
    %meta(http-equiv="Content-Script-Type" content="text/javascript" )
    %meta(http-equiv="Content-Style-Type" content="text/css" )
    %meta(http-equiv="Content-Type" content="text/html; charset=utf-8" )
    %meta(http-equiv="expires" content="0" )
    %meta(name="author" content="MeWho")
  %body{id:@action}
    %h1= @title
    #content= yield