Versatile monitoring and maintenance tool:
System Nucleus
QuickMon
Marxio Timer
Windows Inspection Tool Set
Sysmon

System monitoring and diagnostic:
Best Free System Information Utility
System Explorer
System Information for Windows
What's Running
Change Analysis Diagnostic tool
EVEREST Home Edition
Fresh Diagnose
System Spec
Multimon
Hijack Hunter
System Monitor II
PowerGUI
SystemReport
RegistryReport
SimpleSysInfo
SYS Informer
Sys Information
Karen's Computer Profiler
Xyvos System Explorer
System Information Tool
SystemInfo
SysFile
Son of Snoop on Steroids
WMI-Explorer
Kiwi System Info
BgInfo

Hardware monitoring and diagnostics:
LookInMyPC
PC Wizard
HWMonitor
Sisoft Sandra lite
HWiNFO
SpeedFan
Speccy
CPU-Z
SF Diagnostic Tool
WinAudit
System Information Viewer
Novabench
Crystalmark
Hardware Freak
MiTeC System Information X
Quick Performance Monitor
Auslogics BenchTown
SharpSpecs
thilmera7

Hardware, network and software inventory:
Lansweeper
Spiceworks

Process/startup/etc scanners:
Best Free Process Viewer
Best Free Startup Manager
Autoruns; ASEPMonitor
Process Explorer
Comodo Cleaning Essentials
DTaskManager
Glint
Process Hacker
OTL
Silent runners
Remote Process Viewer
Eusing Utilities
Startup control panel
WinPatrolToGo
Startup Guard
Autostart Explorer
Ez-PC-fix
Atool
Security Autorun
Starter
Startup Manager
Bill2's Process Manager
Ainvo Startup Manager
Auslogics Task Manager
Oolauncher
WhatInStartup
ProcessEye System Utilities
Task ForceQuit Pro
Startup Delayer
TaskManager.xls
System Tray Cleaner
DDS
Free Startup Manager
Puran Startup Manager
Task Manager DeLuxe
SterJo Task Manager
My Startup Delayer
SterJo Startup Patrol
Chameleon Task Manager Lite
Tizer
Kiwi application monitor
Listsp
Anvir task manager
StartupEye
StartupMonitor
Startup Sentinel
Registry Alert
Adlice PEViewer

Process/startup/etc scanners with analyzing help:
ESET SysInspector
OSAM Autorun manager
RSIT
Sreng
HiJackThis; help; portable
OLTPE
Emsisoft HiJackFree
FreeFixer
Hijack Hunter
Run Scanner
Runalyzer
Autorun Angel
x-ray PC
Soluto
StartUpLite
TaskPatrol
Startup Inspector
Universal Virus Sniffer: English version; home (translated to English); review
Quick Startup

Services:
Smart
Advanced Win Service Manager
ServicesSuite
Windows Service Monitor
Service Trigger Editor
Puran Service Manager
svchost.exe Lookup Tool
Easy service optimizer

Device & driver analyzing:
ServiWin
Pserv.cpl
DevManView
DriverView
Device Remover
GhostBuster; review
How to Make a List of the Installed Drivers on a PC

Monitor DLLs:
RegDllView
InjectedDLL
Static Import Finder
Svchost Process Analyzer
FileMap by BB
ListDLLs

Realtime process monitoring:
Whitelist Cloud
Process monitor
ProcessActivityView
SpyMeTools
Top Process Monitor
Fileinspect Sidebar Gadget
Moo0 System Monitor
ExecutableTracker
El Jefe
Process Logger Service

File/folder (hard disk activity) monitoring:
Tiny Watcher
Glint
Directory Monitor
Watch 4 Folder
TheFolderSpy
File Watcher Utilities
What's my computer doing?
FileChecker
AFICK
SysTracer
DiskPulse
Moo0 File Monitor
FolderChangesView
NT Filemonitor
Spy-The-Spy
HDD-Profiler
FingerPrint
Notify
MoniDIR
Track Folder Changes
Windows Explorer Tracker
LastActivityView
Recent Files Scanner
Check5
unhide
Free Folder Monitor
Phrozen Windows File Monitor
Monitor with win7 group policy

Monitor registry and file changes:
MZWriteScanner
RegShot; RegShot Unicode
TrackWinstall
SpyMeTools
RegFromApp
Windows System State Analyzer
WhatChanged
InstallSpy
SystemSherlock
RegMerge
DiffView
RegistryScanner
CRegistry Comparison

Searching files and processes:
file.net
SystemLookup
File Research Center
Process Library
Bit9 FileAdvisor
SANS Institute: Hash Database
ViCheck
Team Cymru
Is This File Safe?
Kaspersky Application Advisor

File type inspector:
TrID; TRIDNet
MediaInfo

Monitor hard disk/SSD:
Best Free Hard Drive Health Monitoring and Diagnostic Programs
CrystalDiskInfo
HD Tune
HDDScan
PassMark DiskCheckup
Acronis Drive Monitor
DiskAlarm
Disk Alignment Test
EASIS Drive Check
SSD Life
Macrorit Disk Scanner
HDDExpert

Monitor memory:
RAMMap
MKN MemoryMonitor
PerfView (also for CPU)
RAMExpert

Monitor CPU:
Process Lasso
Process Tamer

Monitor video card and GPU:
GPU-Z
GPU Caps Viewer
RivaTuner
GPU Shark

Monitor USB activity:
USBDeview
USBLogView
IntelliAdmin USB History Viewer

Group Policy settings:
How to See Which Group Policies are Applied to Your PC and User Account
Group Policy Settings Reference

Event/log viewers:
What information appears in event logs?
EventLog Inspector
MyEventViewer
Windows Event Log Viewer
EventSentry Light
SnakeTail
Advanced Log Viewer
Event Log Explorer

Checksum calculation:
Best Free Hash Utility
Hashtab
MultiHasher
FileVerifier++
HashMyFiles
Checksum Verify
IgorWare Hasher
HashSlash
HashGenerator
ExactFile
MD5 & SHA-1 Checksum Utility
Hashcalc
Karen's Hasher
md5deep and hashdeep
checksum
File Checksum Tool
Marxio File Checksum Verifier
Febooti Hash & CRC
Moo0 Hash Code
Quick Checksum Verifier
VSCryptoHash
QuickiHash
Md5summer
Download Hash Verifier
SDHash
Microsoft File Checksum Integrity Verifier
SFV.net
Hash'em all!
HashCheck
How cryptographic hashing functions work

Search utility:
Best Free Desktop Search Utility
UltraSearch
Everything
Copernic Desktop Search
Wise JetSearch
Locate32
Agent Ransack
DocFetcher
neoSearch
LAN Search Pro
InSight Desktop Search
Mo-Search
Ultra File Search
Miner Mole
VX Search
Quick Search
FileSearchEX
SearchMyFiles
Effective File Search
SwiftSearch
MasterSeeker
Mastering Windows Search using Advanced Query Syntax 
RegScanner
AstroGrep
FileSearchy
grepWin
Dropout

Computer forensic tools:
Forensic Toolkit
Memoryze; Audit Viewer
Mandiant Redline
OSForensics
Disk Investigator
DEFT Linux
CAINE
SIFT Workstation
analyzeMFT
Windows File Analyzer
TCHunt
Encrypted Disk Detector
Fedora Security Lab
Collection of free forensic tools: 1; 2

Integrity checking:
System File Checker tool (sfc /scannow); Run System File Checker Offline
How to Repair Windows 7 System Files with System File Checker
SFCList
Integrity Checker
Rizone File Checker
MicEnum

Digital certificates:
How To Check System Files For Digital Signatures
kSign
How to obtain a digital certificate for free
abylon SELFCERT
AnalyzePESig
ListModules

Monitor errors:
DebugView
WinDbg
WinCrashReport
WhatIsHang
Windows Journal Parser

Resource editor:
Resource Hacker
Dependency Walker
ResEdit

Manage drives:
Drive Manager
USB Manager
FCorp Drive-Thru

Monitor computer usage:
Blackbox Express; review
Spyrix Personal Monitor
Spyrix Free Keylogger

Test system stability:
Heavyload
System Stability Tester
StressMyPC
Video Memory stress Test
Prime95
OCCT
GS Data Generator
CPU heater
FurMark

Other:
ObjMon
Handle Tracer
RequestTrace
RecentFilesView
ShellBagsView
Process Notifier
cFosBark
ProcessThreadsView
API Monitor
WinAPIOverride32
FileInfo
How to Manage Super-Hidden Windows System Files
Hyperball
MindGems Folder size
FS1 collection of tools

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