Becula is fine on Linux [server], but I'd never run it on Windows Server again, it has no effective IO throttling (just number of concurrent jobs throttling, which is ineffective). On Linux you can fix it using security groups with limitations placed on IO specifically (at the kernel level).

It is better at several large files than thousands of small files. In fact when you throw millions of small files at it it chokes pretty bad (CPU skyrockets). So if you need to backup an SQL server data store you'll be just fine, but thousands of XML files? Maybe not.