Deleteing msconfig...

When you uncheck a program/friver load in msconfig, registry modification is done to avoid this to load.
When you remove application, by start/control/remove application, any well written app will remove it's registry dll load too.

If not, you just have to uncheck the line in msconfig, or edit registry to remove the entire line.

Yes, you can delete the programs from the start-up menu.

First, see if you can disable the startup from the settings or preferences menu for the specific application that is listed.

If not, you need to manually edit system files to remove the programs from the startup list.

Start by checking the "legacy" system files using the sysedit command.

You can disable any application started from these files by adding rem and a space to the beginning of the line that executes the program.For most programs, you will need to edit the registry.
CAUTION: Improper use of regedit can cause your system to not boot.
It is 'best' practice to make a backup copy of the registry before editing.

Run regedit from the start menu.
Use file search, and search for runonce
Above and near each instance of runonce, there will be run, run-, and runonce except keys.
The program links that you have unchecked in msconfig will be listed in the run- key
You need to delete each value separately to remove it from the registry and thus the startup list in msconfig.

For more information on the registry, check out the registry pages at Microsoft's TechNet section, or the registry guide at www.winguides.com

Proceed with caution on your first foray into the registry.

Remember, once you delete a value or key using regedit, it is GONE.
There is no undo function.

Chas