Games (ports and exclusives)

Ports
(newly compiled PSP homebrew isn't considered as port as long it wasn't a port itself)
​

First-person shooter
vitaWolfen (Wolfenstein 3D)
vitaQuake (Quake I)
Doom (The original Doom WAD files are needed, its illegal to download them from the internet even when they are so small and easy to find, github)
Doom (PrBoom, prboom_libretro.vpk) (Part of RetroArch, only nightlys atm, just use the Doom above)

Puzzle
2048 (2048_libretro.vpk) (Part of RetroArch, a game, just look here)
Numpty Physics for Vita (A physics based game, Numpty Physics is a clone of Crayon Physics while this is a port of Numpty Physics)

Other
Cave Story (nxengine_libretro.vpk) (Part of RetroArch, a game, only nightlys atm)
EasyRPG Vita (a port of EasyRPG Player, a player for all the RPG Maker 2k and 2k3 games. No creating ability)
vita flappybird (a port of Flappy Bird for Vita)
Flppy Bird (a port of Flappy Bird for Vita, I recommend this one)

Original
(includes remakes, clones, implementations of abstract machines, PSP homebrew compiled for HENKaku, ...)​

Puzzle
BreakVeetOut (A BreakOut clone from Ruben_Wolfe) [v1.0]
PSP2048 (A 2048 clone, there is a 2048-PSP.vpk in the folder)
Flood-It! (A game where you have to flood the whole game board with one color in less than the allowed steps)
MilieTetris (a black and white (and yellow) Tetris clone, simple and straight Tetris fun by Guidobot) [v1.0]
VitaSudoku (a Sudoku game, can have multiple solutions, could be without solution (rare))
Hendoku (a Sudoku game, can have multiple solutions, could be without solution (rare))

Boardgame
ReverseMe (A othello clone)
4Rows (A "Connect 4" / "Four in a row game")
BattleShipArena (A Battleship game)

Other
Conway's Game of Life (Try the Glider , from Ruben_Wolfe) [v1.0]
RejuveSnake (Basic snake game from Ruben_Wolfe) [v1.0]
Tactic Miner (Tactic Miner fell in an unknown cavern. Help him escape. 2D action game. From wonre) [v1.0]
Adventure Time (to share that would be piracy therefore no link here, but there is a unencrypted early version of Adventure Time on the internet its called "Adventure TIme - Very first vita backup.vpk")

Retail/PSN Game Mods/Modding Guides​

Persona 4: Golden undub (Restores japanese voices in non-japanese Persona 4: Golden (cardridge and PSN version))
Final Fantasy X undub (Restores japanese voices in non-japanese FFX copies)
God Eater Resurrection undub (Restores japanese voices in english God Eater Resurrection copies, not complete now, demo video)
The Legend of Heroes: Trails of Cold Steel undub (Restores japanese voices in non-japanese The Legend of Heroes: Trails of Cold Steel copies)

Programs

Shells
VitaShell (molecularShell is a rebranded VitaShell 0.7, no need to install this separately) [Changelog]
molecularShell Disguisers (MolecularShells which spoof to be a Vita game and free param.sfo's, dont forget to delete history and errorlog after installing. From TerraCadenceRedux)

Game-related
RayCast3D Engine (3D Game Engine for Lua Player Plus Vita, it's used for developing games)
EasyRPG Vita (a port of EasyRPG Player a player for all the RPG Maker 2k and 2k3 games)
VITA-8 (a Chip-8 VM, allows to play CHIP-8 games)
VitaPad (Allows to use your Vita as Gamepad, supports Windows, support for OSX and Linux are upcoming)
AntiBlacklist (This homebrew whitelists otherwise unplayable Vita games on the Vita TV, no PSP games. It implements Whiteliste patch v1 and v2)

Privacy/Vita-freeing
AccountSwitcher (Program to swap PSN accounts on a single SD card, allows multiple accounts on one memorycard (alway only one active))
memcardswap (Allows to put memorycards in Vitas/PSTVs with other accounts than used for the memorycard without formating, everything it does is deleteing ux0:/id.dat)
History Deleter (Deletes the Vita game and error history, not only for paranoid people restart the Vita directly after executing this)
molecularShell Disguisers (MolecularShells which spoof to be a Vita game and free param.sfo's, this is only for the paranoid people dont forget to delete history and errorlog after installing. From TerraCadenceRedux)
WebSample (Installs the removed system app "NPXS10916" into ux0, with original bg0 and icon0. From Mooliecool) [v1.0]
Mini Settings (the Mini Settings program that you can't find in 3.60 anymore)
PKG Installer 2.0 (Installs pkgs data which is different from the old pkg format, tutorial from SilicaAndPina, pkgs, more pkgs, install pkgs without a PC from SilicaAndPina)
VitaToolbox (Functions: Swap X/O Button, swap memory card, delete history of started programs and error log, display information about your Vita) [v0.1]
vita-idu (allows to enable/disable demo mode, it can be used for various things like installing the old pkg's.If you don't know what you do you can be stucked in demo mode)
VitaRW (gives read and write access to all partitions, I really hope I don't have to warn you here... github)

Other
MS-DOS Emulator (dosbox_libretro.vpk) (Part of RetroArch, only nightlys atm)
Procedural Planets (Generates pictures from alien worlds which may attack us one day. Aims to imitade No Man's Sky's art-style. Right Button: Generate new Planet - Start Button: Exit, github)
Lua Player Plus Vita (lpp-vita) (Interpreter for the script language Lua. Needed for executing Lua scripts)
FTPVita (A FTP server from xerpi) [v1.1]
VITAident (Display information about your PS Vita)
vita-moddump (allows to dump some PS Vita shared modules, github) [v2016-aug-09]
vitaDump fork by zecoxao (A fork of vita-modump, see one line above. github)
VitaPad (Allows to use your Vita as Gamepad, supports Windows, support for OSX and Linux are upcoming)
HENKaku offlineInstaller (Used to install HENKaku without internet access)
Vita Button Swapper (For swapping the X and O button. This is useful because japanese Vitas use X for cancle and O for confirm)
PKG Installer 2.0 (Installs pkgs data which is different from the old pkg format, tutorial from SilicaAndPina, pkgs, more pkgs, install pkgs without a PC from SilicaAndPina)
vita-moonlight (Allows streaming from PC (Moonlight) to Vita, early version, see here for more information)
VitaToolbox (Functions: Swap X/O Button, swap memory card, delete history of started programs and error log, display information about your Vita) [v0.1]
VitaCID (outputs the ConsoleID (IDPS and PSID) to ux0:CID.bin, can be used for activating Vita on 3.60)
vita-idu (allows to enable/disable demo mode, it can be used for various things like installing the old pkg's.If you don't know what you do you can be stucked in demo mode)
Reboot also known as Reboot shortcat (sic) (It reboots your Vita, from luck)
Vita Activator (can be used for activating your Vita without needing to acces PSN, from ZombieWizzard, remind that you give your account details into a strangers program here, even when ZombieWizzard is a well known dev) [website alternative and PHP script]

Functionality
VitaTester (A simple homebrew for testing the input data on the PSVita. Mostly used to try if your Vita is functional and to try out the API, source code)
Vita Button Test (yet another Vita hardware test program, mostly used by programmers to get used to the new system (libs))
Vita Hardware Test (This is based on Vita Button Test and from the same author. Yet another Vita hardware test program, mostly used by programmers to get used to the new system (libs))
VitaScreenFlasher (A simple Homebrew that is supposed to fix stuck pixels on a LCD TV, better then trying to massage the pixels to live again...)
vitahelloworld (A developer beginners program, hasn't any value for not devs)
VitaToolbox (Functions: Swap X/O Button, swap memory card, delete history of started programs and error log, display information about your Vita) [v0.1]

Emulators

For handheld and console emulators see here. I recommend the bold printed emulators if there is more then one for a console/handheld.
If you want to know more about the RetroArch emulators please consider to visit this thread

The link to my emulator-post above dosn't includes fbalpha2012_libretro.vpk and mame2000_libretro.vpk (MAME v0.37b5) from RetroArch.
Following the hardware which can be emulated using these programs

fbalpha2012_libretro.vpk 

mame2000_libretro.vpk

Non-Console/Handheld Emulators
MS-DOS Emulator (dosbox_libretro.vpk) (Part of RetroArch, only nightlys atm)
ScummVM (<- not="" yet="" but="" i="" would="" like="" to="" see="" a="" port="" from="" the="" psp="" version="" with="" touchscreen="" support="" img="" class="mceSmilieSprite mceSmilie48" title="smile :)" src="https://gbatemp.net/styles/default/xenforo/clear.png" alt=":)" data-mce-src="https://gbatemp.net/styles/default/xenforo/clear.png">)

RetorArch Overlays
Overlays for Gambatte (RetroArch) (just click on DESCARGA, first spoiler for preview)
Overlays for Sega Genesis(?) (RetroArch) (just click on DESCARGA, first spoiler for preview)
Overlays for GameGear (RetroArch) (just click on DESCARGA, first spoiler for preview)
Scanline Overlay for RetroArch
Offical RetroArch Overlays (how to install it?)

RetroArch Icon sets
Icons and liveArea set (RetroArch) (Icon and liveArea set for RetroArch from Melon__Bread)
Icons for RetroArch (for nightly 08.08.16 from Melon__Bread. Copy folders to ur0:/appmeta/ for use)
Icons for RetroArch (for nightly 08.13.16. Copy folders to ur0:/appmeta/ for use)

Related PC programs

Bubble/LiveArea
Icon/LiveArea BUNDLE for HENkaku (Bundle of icons and livearea images)
Bubble Studio (Website for configure bubbles)
Auto-Bubble tool (An automated script that will clone any PSP bubble on your Vita)

Theming
PSVita DB Theme Installer 360 (A easy to use installer for themes, as these or these)

VPK
VPK packer script by Akabane87 (Batch for compiling/converting/... a source code to a VPK. It assumes that the makefile is in the same folder as the outputed velf)
PSDK3v3 (Ready to use Vita SDK for Windows. This is used for development of VPKs. It leaks most of the important libs. Rename PSDK3v3-master to PSDK3v3. Added for completionist reasons only. github)

Host your own HENKaku-Server
Offical HENKaku self-hosting (Host HENKaku localy based on Python and Go/PHP) [Unoffical Docker Version]
HENkaku-webserver (For installing HENkaku without internet, became a lot easier and faster to install than it was with the first release. Compatible with Linux, Windows and OSX plusAndroid.releases)
HENkaku Android (HENKaku server for Android)

Note: If you want to install HENKaku offline from your device see under Programs > Other in these post.

PC<->Vita Backup/File transfer
CMA (the offical tool from Sony, if your PC is online you have to update your Vita, only for Windows and OSX)
QCMA (CMA clone which allows to use transfer data between PC and out-dated Vitas, Support for Windows, OSX and Linux, I recommend this one)
Open CMA (CMA patch which allows to transfer data between PCs and out-dated Vitas) [v5]

Vita game modding/editing
Persona 4: Golden Save Editor (a extensive savegame editor for Persona 4: Golden)
FFXED (a extensive savegame editor for Final Fantasy X HD Remaster (all versions not only Vita))
Phantasy Star Nova Savegame Editor (a savegame editor for Phantasy Star Nova (untested))
GXTConverter (Converter for GXT-format textures used by games for the PlayStation Vita. Maybe intressting for modding)

Other
PSTV PS3 remoteplay files (Files for enabling PS3 remoteplay on 3.60 PSTV, more details)
PSDK3v3 (Ready to use Vita SDK for Windows. This is used for development of VPKs. It leaks most of the important libs. Rename PSDK3v3-master to PSDK3v3. Added for completionist reasons only. github)
Graphical VitaPad Client (A GUI on your PC for VitaPad with some nice features, if you use VitaPad you should take a look)

Other Lists (here included)

Everything you find on following lists should be here too. If you find something on one of these lists that isn't here please post it here.

HENKaku showcase (The list from the hacks official site)
VPK mirror (The legendary VPK mirror)
Hackinformer list (The list in on the hackinformer forum)
PSX-Place list (The list from psx-place)
humbertosnk's list (The list made by humbertosnk)
wololo's emulator list (Now with VPKs)

/r/vitathemes (vitathemes subreddit, not included here)

Outdated VPKs with indirect successors

Outdated

RetroArch REPACK
Smoke5's MolecularShell MOD (Modded version of MolecularShell which allows access to more folders, substitutes the original MolecularShell's bubble) [based on VitaShell 0.6]
Voxel Studios MolecularShell MOD (Modded version of MolecularShell which allows access to all folders, VPK installation broken in these Shell, adds new bubble instant of substitute the original MolecularShell's one) [based on VitaShell 0.6]
Vita TV whitelister (This homebrew whitelists otherwise unplayable Vita games on the Vita TV, no PSP games. From Kankertje) [v1.1]
Moon Whitelister (Yet another whitlister, does the same job as the program one above)
molecularShell Update (installs VitaShell 0.7 in molecularShell-bubble (substitutes molecularShell), from atreyu187)
[memcardswap icon version based on v1.0]

PSN update blocker
VitaUpdateBlocker (allows to connect to PSN with 3.60 without the need to update, this tool will work only a couple of days)
PSProxy (allows to connect to PSN with 3.60 without the need to update, this tool will work only a couple of days) [v3.0.0.0]