Entity Framework + SQLite deployment

You're unlikely to be reading this anymore, but you're missing the following in your app.config (or, for you, web.config):

<configuration>
  <system.data>
    <DbProviderFactories>
      <remove invariant="System.Data.SQLite" />
      <add name="SQLite Data Provider" invariant="System.Data.SQLite" 
           description=".Net Framework Data Provider for SQLite"
           type="System.Data.SQLite.SQLiteFactory, System.Data.SQLite" />
    </DbProviderFactories>
  </system.data>
</configuration>

Specifically, if you're using sqlite in a library which is linked into your website, you must add this to the config file of the website - not the library! This is because of how you're loading the provider: essentially, you're determining at runtime which dll to load, using the string "System.Data.SQLite", and locating the appropriate provider is done using the settings of the entry assembly.

Edit: By the way, when you're writing the library that has an sqlite dependancy, you can avoid this complexity. You do not need to use DbProviderFactories to look for sqlite at runtime; you can take a compile-time dependancy just as well, which can be easier to manage. Then you can ignore the above app.config section, and instead replace all instances of:

DbProviderFactories.GetFactory("System.Data.SQLite").CreateConnection()

with

System.Data.SQLite.SQLiteFactory.Instance.CreateConnection()

If you do so, you're using a plain library call to create the connection and there's no runtime selection of db provider. That can be less flexible since you can no longer exchange data providers via the config file, but for many libraries that's sufficient. Unfortunately, if you don't control the library code, this isn't an option.

Have you tried adding the required DLL(s) to your application's bin directory? You might want to look at Phil Haack's article on Bin Deploying ASP.NET MVC for ideas on how to do this automatically.

SQLite needs full trust permission for ASP.NET application deployment. Many shared hosting providers don't allow that. You might wan't to check this.