Can I store any custom tables in SharePoint's own database?
Is this supported behavior or not?
(I mean tables in MS SQL database, not SharePoint lists.)
If I can, how well does this play with backup/restore functionality?
What are possible caveats?
For anyone wondering why I'm asking: there's an app which is bound to SharePoint server and needs to store some purely relational internal information that doesn't make sense apart from that SharePoint instance. I would like to narrow down data storage to one place but I'm not sure if SharePoint likes its database being used for other purposes.
I'm using SharePoint 2007.
Is it possible? Sure. Should you? Nope.
The SharePoint content/configuration databases are subject to change with any update Microsoft releases, and any changes you make will very likely be destroyed, and if your farm depends on them, be left non-functional.
If you want to store purely relational data in a set of tables, just create another database. There's nothing stopping you from using the same SQL Server instance that houses your SharePoint content and/or configuration databases to store other relational databases as well.