It sorta sounds like your looking for a central authentication service/server that many applications would use to authenticate?
The different databases thing does throw me. Are you saying upon authentication, the user would have access to a particular database? Or are you saying multiple identity stores to authenticate from?
For a centralized authentication solution I would suggest identity server (WIF) both/or authorization server (OAUTH) from thinktecture. Each application would be a relying party.
If you really want to do a custom owin solution, you can do a single api solution that does bearer authorization and use that token in your other applications but you would need to implement ISecureDataFormat so that each application can decrypt the token to to get the identity and each application would have to share the same userstore.
Just a heads up, decryption doesn't really mean you can trust a token, it really should be signed and verified to have complete trust. depends on your needs and risk you're willing to take.