The dreaded duplicate entries of msconfig
............and what to do about them:
Easiest way to get rid of duplicates in the startup tab: Check them all and then use apply/ok/reboot. All
"real" duplicates will be eliminated.
Now, to address the real matter: For each entry left, check the associated program for an option not load at startup and undo it. Look for something like "allow to run in system tray" or "allow to run in the startup group". The duplicates you are seeing in the startup tab is the result of not doing this in the first place. Many programs will simply rewrite the entry if not disabled properly.
Then, after completing that step, you can go back to msconfig and disable whatever is left that you could find no option for, refer to this page: Cleanup Your System. Be aware that some duplicates are by design, a particularly notable one is "load power profiles" and both entries should remain enabled, the explanation is below.
For the last part, if there are entries for programs which are no longer installed on the computer, and you did correctly uninstall the program (not just deleted the program folder, which can cause a whole host of problems), then you can remove the "dead" entry by editing the registry:
Start/run regedit, navigate to these keys (not all may exist in all systems):
and look for the disabled lines in the keys ending with a minus sign (-). Delete the strings in the right-hand pane representing those programs. I would suggest exporting a copy of any string before you delete it just in case its' removal causes any problem (it shouldn't, but this is a good habit to get into when you are messing with the registry).
*NOTE* Please use caution when working within the registry. Changes made here are generally immediate. Making the wrong change or carelessly changing/deleting keys can render your system unbootable. If you are unsure about any change, don't do it. Before you make any changes to the registry, know how to backup and restore the current one from a command prompt.
Now, many times I see a question regarding "Load Power Profiles" and why is it there twice. This is by design actually. One entry originates from Run Services in the registry, the other from a Run key. The first loads a set of "default" settings for power management. The second loads the user-specified ones. Disabling one or the other often causes any system setting changes to be "lost" when the user reboots. This is why neither of them should be disabled. This is true even for a single user system with no Windows logon, the logon in these cases is automatic and unseen, but it still exists.
Some registry pages that are very useful include:
Description of the Windows Registry Checker Tool (Scanreg.exe)
Command-Line Switches for the Registry Checker Tool
How to Manually Restore the Windows 98 Registry