All versions of Windows since 98 (98 SE, ME, XP and Vista, excluding 95, 2000 and NT) have the System Configuration utility, also known simply as msconfig. Not much has changed in it except which system files it configures.
I’m going to give a quick rundown of every tab in the msconfig window.
First thing you need to do is open msconfig. To do this, click Start > Run and type in msconfig then hit enter. You should then see this:

This tab is for selecting how Windows is going to boot. The first option is self explanatory. I have never seen Normal Startup selected, though I image it is the default option selected after a fresh install of Windows.
The next option is Diagnostic Startup. I’ve never used this option before, but it seems to be pretty similar to Safe Mode. Some of the services that this disables is Networking, Plug & Play, Event Logging, and Error Reporting. And according to Microsoft, this also permanently deletes all system restore points. So keep that in mind if you ever decide to use this.
The next option is the one that is always selected on my computers, Selective Startup. The first two sub options should be checked. The second two sub options will be checked if you have never changed anything under the Services or Startup tabs, if you have, they will be green like in the picture. The next sub option just tells Windows whether or not you are using the original boot.ini or a modified one. You will not be able to select modified unless you modify the boot.ini file from within this program (the boot.ini tab). If you edit it manually by opening it in notepad, msconfig will still think it is the original. More on boot.ini later.
Next tab: SYSTEM.INI

First thing you should know about this tab and what’s in it is this: DON’T CHANGE ANYTHING. This file has pretty much been phased out in favor of the registry. In a fresh install of XP, this file is created blank, but XP will still acknowledge some entries to provide backwards compatiabilty with older 16-bit applications.
Next tab: WIN.INI

First thing you should know about this tab and what’s in it is this: DON’T CHANGE ANYTHING. By default in Windows 3.x, basic settings were stored in this file, but like system.ini, it was phased out in favor of the registry. Also like system.ini, XP will still acknowledge some entries to provide backwards compatibility with older 16-bit applications.
Next tab: BOOT.INI

If you use Vista, skip this. Vista did away with the boot.ini file and now stores information for manging boots in the registry.
Boot.ini is the only boot file you would ever need to worry about, and really only if you are trying to do dual boot. Boot.ini contains several things Windows needs to know as it boots. Editing the file from here will change the option under the General tab to “Use modified BOOT.INI.” First entry is timeout. If you have multiple versions of Windows (or Windows and Linux, though using boot.ini to boot Linux sucks and isn’t really done anymore), the value for timeout is the length of time, in seconds, it will give you to select which OS you want to boot. The next entry is default. This tells Windows what OS entry you want to be the default. If you fail to make a selection before the timeout period ends, the value for default will be used.
The next section lists the operating systems installed. Each line is a separate entry and these will be displayed at boot up. Here is an example of a boot.ini with two OSes:
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)..WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)..WINDOWS=”Windows XP Professional” /fastdetect
multi(0)disk(0)rdisk(0)partition(2)..WINNT=”Windows 2000 Professional” /fastdetect
The checkable options add the value to the end of the selected OS giving it various different commands for booting said OS. Here’s a rundown.
/SAFEBOOT – Safe Mode
/safeboot:minimal – Enter safe mode with minimal device drivers.
/safeboot:miniaml(alternateshell) – Uses an alternate shell (interface).
/safeboot:network – Adds network support.
/safeboot:dsrepair – Starts a domain controller in Directory Services Restore Mode.
/NOGUIBOOT – This disables the bitmap progress bar when booting. This also disables the text output used by CHKDSK and various partitioning tools, so you should use this switch with extreme caution.
/BOOTLOG – Creates a log file to log the boot process.
/BASEVIDEO – Starts the computer using the standard VGA video driver instead of the video driver from the video card manufacturer.
/SOS – Names the display drive while loading.
Clicking Advanced Options brings up yet more command options.
/MAXMEM=nnn – Sets the highest memory address Windows can use
/NUMPROC=n – Sets the number of processors Windows is allowed to use. This is useful if you have a processor that is defective or failing. This applies to multi-core processors as well. What I’m not sure about is how you can tell it which proc to use and which one not to use.
/PCILOCK – Tells Windows to let the BIOS assign device addresses instead of Windows.
/DEBUG – Causes the kernel debugger to load and activate.
/DEBUGPORT=comport – Debugs a certain port.
/BAUDRATE=n – When a com port (com1, 2, etc) is selected this option becomes avaliable to set the baud rate used.
/CHANNEL=n – If 1394 is selected as the port, this allows you to set the channel used.
For more command options, see this.
Next tab: Services

This contains a list of all services that have a Startup Type of Automatic or Manual as listed in services.msc (which has a complete list of ALL services whether set to Automatic, Manual, or Disabled). As long as the service does not say it’s essential, you can de-select it from starting up with Windows, however doing so may cause weird things to happen if the service has something to do with Windows functionally. Some people thing that cleaning out this list to only include services vital to Windows will speed up boot time and free up system resources. Not so much. If it is from Microsoft, I’d leave it be, but feel free to un-check any third party services. This tab also tells you what the current status of the service is, Running or Stopped. A lot of services will run at boot to serve some function then shutdown shortly after, others remain running all the time. These services are started before you get to the login screen.
Next tab: Startup

This lists all programs that are set to startup with Windows. This includes Microsoft programs as well as third party apps. Anytime you tell a program to start will Windows, it simply adds an entry here (which is actually in the registry) telling Windows to boot it at startup. This is done about the same time as the desktop first appears. This is a good place to come if you have a slow boot up. Taking programs out of here can have dramatic effects in your computers start up time if the program is a resource hog or simply isn’t working right.
For more information check out the following links:
How to Edit the Boot.ini File
How to Troubleshoot Configuration Errors in Windows XP by Using the System Configuration Utility
How to Troubleshoot Configuration Errors in Windows Vista by Using the System Configuration Utility
Also, special thanks to Jesse for recommending msconfig as a topic.