Hi,
I've noticed a ticket on the wiki for per-user tool permissions: https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-to...
If anyone is interested, the following patch implements such thing (but requires manual code changes whenever the access needs to be changed). The method "tool_allowed_for_user()" can of course be extended/rewritten to read access permissions from file or from a database.
Comments are welcomed, -gordon