So, here is my list:
Note: feel free to add your tools to my list. If it's an alternative, please don't replace mine, add a sub-list started by "alt:" and say why do you prefer this one.
Boot-cd/usb key
* Ubcd4win create a (custom) live cd with many good tools
* Offline NT Password & Registry Editor reset windows password
o alt: Ophcrack (sort-of) brute-force windows password (if they are EFS encrypted files)
* CloneZilla disk imaging backup
* GParted partition editor
* Stresslinux minimal linux with tools to monitoring hardware health: stress, cpuburn, hddtemp, lm_sensors, memtest86+, ...
o alt: Memtest86+ RAM tester (don't need command line)
* Hard Drive Manufacturers diagnostic tools: fujitsu / hitachi / samsung / western digital / seagate (maxtor)
* Spinrite hard disk recovery (89$)
o alt: HDD Regenerator (40$)
o alt: TestDisk (Free) designed for repairing corrupted partition tables
* Microsoft Emergency Repair Disk: a system rescue disk PE environment with advanced recovery tools like resetting passwords, hard drive repair, offline registry editing, file explorer, command prompt, etc. Only available to Software Assurance and MSDN subscribers, as part of the Desktop Optimization Pack. If you're a student, may be available to you through MSDNAA.
Kits
* Sysinternals suite (1=included in this suite) a great set of tools by Sysinternals (so great that MS bought them)
* NirLauncher (2=included in this suite) another great set of tools by NirSoft integrated in a launcher (that could be used easily with sysinternals suite too)
* GnuWin32 port of the most important GNU utilities to Windows (command-line)
Remote control
* Teamviewer all-in-one solution for remote access and support over the Internet. Easy (don't have to open ports on firewall/router), secure, and full featured.
o alt: UltraVNC: less convenient but open source and free even in a professional environment
Anti-malware
* Avira (use rescue disk or the one included in ubcd4win) and/or Kaspersky Virus Removal Tool
o alt: Malwarebytes' Anti-Malware / SpyBot - Search & Destroy / DrWeb Cure It / AVZ / a-Squared Emergency USB Stick
* Microsoft Security Essentials or Avira (a little bit better but contains nag screen) -to install
o alt: Avast / AVG
o alt not freeware: Norton Internet Security (70$/year) / Kaspersky Internet Security (60$/year) / Eset Smart Security (48€/year) / PC Tools Internet Security (50€/year)
* System Explorer lists processes, startups, services, drivers... Check them with it's own database, VirusTotal or Jotti services. Snapshots before/after for registry/disk changes
* RootkitRevealer(1) anti-rootkit
o alt: Gmer more powerfull (but harder to use) anti-rootkit
* Virus Effect Remover Repair/Fix damaged items like TaskManager, RegEditor, Folder Options, Windows AutoUpdate.
Startup Tools
* Autoruns(1) the most comprehensive knowledge of auto-starting locations of any startup monitor
o alt: RunAlyzer edit an external registry hive (used easily from a boot cd)
Process Tools
* Process Explorer(1) detailed process, handles & dll informations
* Process Monitor(1) real-time file system, registry and process/thread activity
* Svchost analyzer lists all svchost instances and checks the services they contain
Registry Tools
* Registrar registry manager (lite) advanced registry manager
o alt: Reg
* Eusing free registry defrag
Backup Tools
* DriveImage XML disk imaging (shadow copy)
* Cobian Backup automated backup -to install
* Toucan on-demand backup
* ERUNT registry backup
* SingleClickRestorePoint
* Netprofiles save & restore network profiles
* SoftKey Revealer licence keys backup
* All Nirsoft password tools(2) passwords backup
File Tools
* Everything quick searching
o alt: AstroGrep for non-ntfs drive
* Recuva recover delete files
* RichCopy advanced copy tool
o alt Unstoppable Copier copy files from broken hd
* FileASSASSIN advanced delete (remove handle or delete at reboot)
o alt: Delete Doctor delete with short DOS name or UNC name
o alt: DelinvFiles same as delete doctor, but can scan the drive for invalid file names and from my experience it was successful where delete doctor wasn't. But it's a shareware: 26.95$
* WinDirStat: graphical view of hardrive space usage
o alt: SpaceSniffer nicer interface
o alt: SequoiaView
* WinMerge folders/files comparison
* Hashcalc md5,sha,crc32 checksum
* TrIDnet file identifier
Hardware Tools
* SIW display detailed informations about the system properties and settings
* IntelBurnTest test cpu
* FurMark test gpu
* Eizo Monitor Test fine-tune your monitor
* Pixel Doctor locate and fix LCD screens dead pixels
Drivers Tools
* DoubleDriver backup/restore drivers
* DPC Latency Checker real-time drop-outs graph
* DeviceRemover (very) advanced device manager
Disk Tools
* Drive Manager
* MyDefragPowerGUI featured (& free) defragmenter
* HDTune hd scan & S.M.A.R.T. info
o alt: Active@ HD Monitor freeware more featured, but not portable
* Easeus Partition Master (home edition) partition manager
Cleaning Tools
* RevoUninstaller uninstaller that help to remove leftovers (without the need of monitoring install)
* CCleaner remove unused and temporary files
* PC Decrapifier remove or uninstall a specific list of unwanted software
* JavaRa removes old and redundant versions of the Java Runtime Environment
Network Tools
* NetWorx bandwidth meter
o alt: NetMeter the live graph looks better but is a little less featured and have some instabilities on w7
* NetResView(2) lists all network resources (computers, disk shares, and printer shares) on your LAN
* CurrPorts(2) lists all currently opened TCP/IP and UDP ports and the processes that opened them
* AS3 Personal Firewall portable firewall
* eToolz gui for NS-Lookup, Ping, TraceRoute and Whois
* Performance Pinging graph ping
* Wireshark network protocol analyzer
* Secunia PSI vulnerability scanning
* SG TCP Optimizer (XP) (re)set & optimize tcp parameters
Misc
* SUMo software updater tool
* BlueScreenView(2) crash dump analysis
* ShellExView(2) shell extensions manager
* Whyreboot lists reboot "pending file operations"
* XP Quick Fix Plus 40 common Windows XP problems fixes
* 7 Quick Fix 21 common Windows 7 problems fixes
* thewindowsclub.com fix tools: FixWin (50 common 7/vista annoyances), Fix IE (internet explorer), Fix MSE (ms security essential), Fix WU (windows update), Fix WMP (windows media player), File Association Fixer
* GodMode creator (7/Vista) create easy shortcuts to almost every settings & informations (CLSID folders)
* Print Service Manager easily kill stucked print jobs
* Filmerit directshow filter manager
* System Info for Windows gives a ton of information about the system, including installed software, hardware configuration, license keys, and network info. Free for non-commercial use; $70 for "technician's license".
And some other essential tools, but not directly related, like notepad++, autohotkey, firefox (and its bookmarks)...
Most of these tools are portable and free (at least for personal use) and yes it's only the essentials one
And if you want more security related software: Gizmo's Best Free Security List (by Antti Koponen)
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