When you are not using the entity framework, you will only need the "System.Data.SQLite.dll" (for the correct platform [x86 or x64]).
When your application is targeting "Any CPU" the "System.Data.SQLite.dll" (x86 and x64) will need to be installed to the GAC to let it pick the right version.
When using the entity framework, you will need "System.Data.SQLite.dll" and "System.Data.SQLite.Linq.dll". Also the provider needs to be registered:
In app.config or globally in machine.config
<?xml version="1.0" encoding="utf-8"?>
<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>
The source is available here:
https://bitbucket.org/ionkiwi/sqlite.net4