Spybot is a spyware detection, and removal, program.
It also has a couple of other useful features, such as a startup monitor, and TeaTimer, which monitors the registry, and prevents unauthorized changes.
Programs, and files, are not interchangable terms.
A program would be like Internet Explorer, Spybot, Photoshop, Windows Media Player, etc.
Programs contain folders, which contain other folders, and individual files.
What Microsoft has to say about using msconfig:
Microsoft strongly recommends that you do not use System Configuration Utility to modify the Boot.ini file on your computer without the direction of a Microsoft support professional. Doing so may render your computer unusable."
In fact, microsoft specifically warns not to use any application unchecked in MSCONFIG startup until the entry is rechecked and the computer restarted.
If microsoft actually thought that MSCONFIG were safe to use as a startup manager, it would not be hidden.
There would be an entry in the control panel and in Start/ Programs / Accessories called, "control startup programs here".
They do not hide components because they are mean, or because there is a mysterious conspiracy between geeks, to make it hard on others.
These are hard to get to, and hidden, because they are dangerous, and should only be used by a professional who understands the potential risks, of his
The best way to manage startup items is within the programs own options/ preferences.
Any well written application will have correct methods of doing this, to correct the entry points, and memory management, as the softwares author intended.
The next best alternative, is a third-party startup manager.
This is my opinion.
I'm sure others will have a different opinion, as this is usually a hotly contested topic.
In regards to system files that have to run at startup, they are not programs, so I assume you are not referring to these types of files when you talk about disabling programs via options....???
I'm only talking about unnecessary programs running at startup, that can be started manually, if necessary, such as Word, Quicktime, etc.