I've worked at a place that had a large number of orphaned and semi-orphaned databases. It was hard to tell if they really were orphaned as many tasks were seasonal or annual - so that website only runs for 3-4 months per year (as an example, W2 forms need to be electronically filed 1/31, so the website processing these only ran from mid January to the end of April).
What was done was a combination of:
* ask every developer if they were using some database or the other (these emails would go out monthly or whenever backups were taking too long).
* take the database offline and see who complains.
* rename the server to see who complains.
Since the pointy haired boss only was willing to allow "full and complete" documentation, a wiki was expressly forbidden, and staff reductions lead to a dramatic decline in documentation that met the standard.
If it were up to me, there would be a wiki page per server with contact names for each database (and maybe a brief description of what the database is for). Any database undocumented on the wiki would be fair game for deletion.
We had one large financial client that was still using SQL Server 2000 as late as 2009, so we had to keep one SQL Server 2000 instance running until that client finally moved to SQL Server 2005.