Can anyone recommend a database backup utility, free or paid? Ideally it will
backup MSSQL & MySQL, but MSSQL only will suffice
allow backup of single tables
There isn't a tool which allows for a backup of a single SQL Server database table. You can export each table using BCP however these wouldn't be consistent with each other and wouldn't be a viable backup model.
Native database backups can be encrypted if you enable TDE in SQL Server. You can also use third party products like HyberBac, LiteSpeed, SQL Backup to encrypt (and compress) backups.
I don't know of any floss tools that will do that for both MSSQL & MySQL. You might want to take a look at http://www.r1soft.com/windows-cdp/. Their product for Linux works but involves loading a binary blob into the kernel "tainting" it, which may be a vendor support issue for you. I won't run binary blobs on production servers.