What are best practices for safely permanently deleting a database?
You could try to set up a trace that only captures connections and to what database they connect to. I would leave this running for a bit and then make sure nothing is connecting to it.

One problem with that would be if you have some code opening up on the master db but calling another DB within the code. I'm not sure how bad the code is that is pointing to your DBs.

I'd also query all your jobs and make sure none are pointing to that DB

You could also use SQL audit if you have the right version of SQL (2008 R2 enterprise).

You could also use logon triggers to update a table when someone logged on to that DB. This would show you if anything was connecting to that DB.