Small steps to protection:

Intro:
To remove crap is first part of way other part is to get it work again. Clean reinstall is the simplest way but not the best and not always. But if you have backups of necessery files so you can use them to get you system back after reinstalling of windows

Begin:
Run scandisk before and after reporation("chkdsk /f") to check that it is no errors on you harddrive becouse if it is some there, so them can lock access to files on you harddrive. Empty temporary files and disable "System Restore". Defragment disk is also good idea after removing of crap(malware,temp) files, this will increase speed if windows.

"cmd" and "command" is same exept that "command" is using just in "Windows 9x" and "Windows ME" for going into console mode(command line).
In console you can also use "help" command to se what windows commands you can use.
To get more info about what switches intrested command have you can use "/?" switch:
t.ex. "cmd /?" or "help cmd"
few other switches for help that supported by some other programs is "--help" "-h" "?" or just empty(no switches).

With "mmc"/"computer manager" you can add modules and watch information about you computer and configure windows monitoring tools. "Logbook" contains information about common errors in you computer. But not all of them are critical.

To get more info about what errors means you can look at microsoft page
http://www.microsoft.com/technet/sup...ntserrors.mspx

Not mine but usefull tuts:
1)"Usefull Google tips" by Faqt
http://www.antionline.com/showthread...hreadid=229155

2)"Asking smart questions" by pwaring
http://www.antionline.com/showthread...hreadid=231720

3)"Whoa, did you know Win2K had a comand line?" by breakology
http://www.antionline.com/showthread...hreadid=247874

4)"Computer Infections – Definitions, Vulnerabilities and Prevention Assistance" by Relyt
http://www.antionline.com/showthread...hreadid=258222

5)"Trojans/ Backdoors - My observations" by slarty
http://www.antionline.com/showthread...hreadid=243202

6)"Adware and Spyware removal :Introduction:" by foxyloxley
http://www.antionline.com/showthread...hreadid=265440

Those tuts are basic help.

Then when you computer is clean you still may have some problems, like some windows functions not working or other programs stops to work properly. In windows hawdrware manager you can se if some errors are there.
In that case you may need to reinstall some of windows componets(depends on what not working):
1) windows script (if for example "search for files" not working)
2) drivers for network card if not getting ip.
3) runs "SFC /scannow" from "run" menu or console(cmd)
4) register unregistred dlls
->>
go into console mode ("cmd")
go into windows\system32 ("cd %windir%"\system32)
create list of dlls ("dir *.dll *.ocx /s /b > dlltoreg.cmd")
open dlltoreg.cmd for editing ("start wordpad dlltoreg.cmd")
replace all "C:\" with "regsvr32 /s C:\"
run dlltoreg.cmd ("dlltoreg.cmd")
open task manager ("ctrl+alt+del" or "ctrl+shift+esc")
if "regsvr32" freezing for more then 1 minute then kill it in taskmanager so it will continue to register other dlls.
When it is completed reboot computer.
If some new or other dlls that couldnot be found by first time of cleaning will registry again. So you can repeat removal steps. AV's and anti-spy's is using registry to track them down by known ID's in windows registry.
<<-
5) Clear registry by some regcleaner("RegCorrector").

If you have no hardware problems then you computer will work fine.