Those in msconfig that you see are in the registry, although they are not all there is. You can try read
/Software/Microsoft/Windows/CurrentVersion/Run
and
/Software/Microsoft/Windows/CurrentVersion/RunOnce
In both HKEY_LOCAL_MACHINE
and HKEY_CURRENT_USER
You can find information about those at MSDN and support.microsoft.
Try the article Read, write and delete from registry with C# at CodeProject to get you started with the registry.
Now, as I said above, they are not all there is. Listing those will still miss services and drivers, and also some other code that will start async, such as Explorer extensions, Control Panel extensions, codecs for audio and video among others. All that without considering that the client machine may not use explorer as shell.
I recommend you to have a look at autoruns at sysinternals. You can also use its command line tool to get the info you want.