Having certain programs run at start up can be convenient, but it also uses memory and can slow down your computer. Generally, the programs accessible in the "Startup" tab of msconfig--the Microsoft System Configuration Utility--are not required in order to load the operating system, but disabling certain ones can prevent software from functioning correctly, and can cause hardware incompatibility. Therefore, you should not prevent programs from running at start up unless you know what they are, and you are certain that doing so will not affect the performance of your computer.
Generally, components vital to Windows functionality will not appear in the Startup tab of msconfig, but sometimes they do, particularly when running older versions of Windows. For example, you may see one or more copies of LoadPowerProfile in the Startup tab, which maintains the power settings for your user profile. Although disabling LoadPowerProfile would not prevent the computer from starting up, the computer would lose the power profile functionality. Sometimes you will also see Explorer in the Startup tab, which is the Windows graphical user interface--a much more vital component. Disabling Explorer from running at start up would prevent you from accessing the Start menu or browsing through folders.
Anti-virus programs, firewalls, and other types of software designed to maintain computer security should run at start up, assuming you want their protection constantly. Although you do not technically need to run any of these programs at start up in order for Windows to load properly, if you choose to disable them, you will need to start them manually in order to benefit from their functionality.
When you install hardware, drivers and programs associated with that hardware will sometimes be set to run at start up by default. For example, Logitech keyboards and mice typically come with SetPoint, a program that allows you to program special buttons and button combinations. Thus, if you use a Logitech keyboard or mouse, and you prevent SetPoint from running at start up, you will not be able to benefit from any of the enhanced functionality. Similarly, some software requires the installation of drivers that must run at start up. One example is Daemon Tools, a popular drive emulation program. If you disable Daemon Tools from running at start up, the emulated drive will no longer be recognized.