Signing out deletes data and authentication tokens from the cache, and it also deletes cookies on iPad and Android tablets. Signing out does not delete metadata. This means that if a user signs in again after signing out, a metadata sync is not required before using the application again, which can save a few minutes when you sign in.
CRM for tablets makes a best effort to delete data and authentication tokens from the cache; it is not guaranteed that this will occur in every situation.
Reconfiguring deletes all data and metadata from the cache.
If you sign out from one organization and sign in to another, and use the Reconfigure option on the second one, your metadata will still remain for the first organization. If you want to remove your metadata from the first one, you'll need to sign in to it and use the Reconfigure option there, as well.
CRM for tablets makes a best effort to delete data and metadata from the cache; it is not guaranteed that this will occur in every situation.
Note about pinned tiles
If you're using a Windows 8 or Windows 8.1 tablet and had pinned tiles to your Start screen, those tiles will remain whether you use the Sign Out or Reconfigure option. These tiles will only work for users who have access to that record or view, however. For example, if you sign in as user1 from org1 and pinned a tile to Start, someone who signs in as user2 from org2 and taps that tile will receive an error message saying the record isn't available.