Apparently it's a common problem (who knew!) that a lot of people don't understand what patching actually is, so allow me to explain the logic of patching.
Patching is the process of adding new information or code over the old information or code with the intent of bringing the package up to the equivalent of the current version. The process isn't magic, you can't just change the final version and expect it to be correct. Let's do a visual example:
Say the first 3x2 rectangle is the videos folder, the second is music folder, and the third is the packages folder.
Code:
▓▓▓ ▕░░ ▏ ██▓ ▕ ▏ ██▓
▓▓▓ ▕ ░ ▏ ▓█▓ ▕ ▏ ▓█▓
▓▓▓ ▕░ ▏ █▓▓ ▕ ▏ █▓▓
▓▓▓ ▕ ░▏ ▓▓█ ▕░ ▏ █▓█
▓▓▓ ▕ ░░▏ ▓██ ▕ ▏ ▓██
▓▓▓ ▕░ ▏ █▓▓ ▕ ░▏ █▓█
115 115->116 116 116->117 117
If you look at each full version (115, 116, and 117) you can see what the expected result is. 115->116 is the patch, what we call a difference between the two versions. You can visually see here how ▓ + ░ = █
So what happens to the silly billy that doesn't understand the logic, and tries to apply 116->117 over 115?
Code:
▓▓▓ ▕ ▏ ▓▓▓
▓▓▓ ▕ ▏ ▓▓▓
▓▓▓ ▕ ▏ ▓▓▓
▓▓▓ ▕░ ▏ █▓▓
▓▓▓ ▕ ▏ ▓▓▓
▓▓▓ ▕ ░▏ ▓▓█
115 116->117 ERR
That sure doesn't look like the 117 we wanted, does it? 
Hopefully that explains what patching is and how it works. Tell me if it doesn't, and ask me for the clarification you need so I can add it.
ATTN: If you're just installing a manual patch DON'T READ THIS. (DERP) This a tutorial for my successors as much as it is a release thread. SCROLL DOWN FOR RELEASES AND INSTALL INFORMATION.
This is a quick how-to on how to grab your own manual patches. Also links later.
Anyway, everyone who has to manual patch knows how much Nexon sucks at making manual patches, so here's how to make your own.
First of all you need a modern browser or an FTP client (I suggest FileZilla).
Connect to ftp://mabipatch.nexon.net/ by either clicking that link, or if you're using an FTP client, entering that in its proper fields.
You'll see a list of folders with numbers for names, these are the game's version numbers. Find the latest and open that one.
In that folder are a bunch of files that say XX_to_YY.Z where YY is the same number as the folder name and Z is the part number. Look for the one where XX is the version number of the Mabi you have installed. Download all of these (where only Z changes, so if you have 74 and the latest is 76, download 74_to_76.0, 74_to_76.1, 74_to_76.2 etc).
Then scroll to the very bottom of the listing and download YY_language.p_
Go to the folder you downloaded these files into. Rename YY_language.p_ to YY_language.zip
How to make the patch (Windows)
Now open command prompt (Start->Run->cmd) and navigate to this folder (type "cd " without quotes then drag and drop the folder into the cmd window).
XP?/Vista?:
Now in command prompt type "copy " then each XX_to_YY.Z file name with a + in between them and end with " XX_to_YY.zip /B"
For example: copy 74_to_76.0 + 74_to_76.1 + 74_to_76.2 74_to_76.zip /B
Windows 7:
Now in command prompt type "copy /B" then each XX_to_YY.Z file name with a + in between them.
For example: copy /B 74_to_76.0 + 74_to_76.1 + 74_to_76.2 74_to_76.zip
You can then delete all the XX_to_YY.Z files, and with your last two zips remaining, you've made a manual patch! 
How to make the patch (Linux)
Open terminal and cd to the folder with all the pieces in it.
Run the following
1) rrn 'XX_to_YY.?' 'XX_to_YY.0*'
2) cat XX_to_YY.?? > XX_to_YY.zip
Be sure to test the zip, but you won't be able to extract it very well due to the path separator being a backslash instead of a forward slash. (I mean, it'll extract, just not maintain a proper tree.)
How to make a new version.dat
Download this.
Run mabiver.exe (Windows) or mabiver (Linux) in your Mabinogi directory. It will print the current version number and request a new one.
WARNING: This currently does not work by double clicking, run it from cmd.
That is, open cmd and run the following:
1) cd C:\Nexon\Mabinogi
2) mabiver
Included is the source and both compilations, as well as a version.dat to use it on if you don't want to use it in your Mabinogi directory directly.
Credits to this post that I randomly came across while helping people in IRC with this patch stuff, and made me realize there's a version.dat file in the folder. I honestly didn't see it there. =__= Easy to figure out but I would've felt bad not giving credits.
How to make the bypass shortcut
To run Mabinogi now you must use the launcher bypass, as this method does not update whatever is necessary to make the launcher not try to update, itself.
To do this, make a new shortcut on your desktop and change the target to:
Code:
C:\Nexon\Mabinogi\Client.exe code:1622 ver:94 logip:8.31.99.11 logport:11000 chatip:8.31.99.12 chatport:8002 setting:"file://data/features.xml=Regular, USA"
(Thanks for the copypasta Skitty <3 I forgot to write that down. ^^; )
This assumes that's where you installed Mabinogi (it's the default folder, you shouldn't install it anywhere else!)
Version (ver) is ignored, however you may update it with each patch if you like. In the above, it corresponds to YY. Login server IP (logip), port (logport), Chat server IP (chatip), and port (chatport) are subject to change however. You can get the latest information for the bypass here. This is what the launcher uses to start Client.exe.
Automative Scripts
Download the script for your system and mabiver into a directory.
Download the patch files into a folder mimicking the FTP's structure (eg. a folder named the game version) that's in the folder with the scripts and stuff. Unpack mabiver in the same folder as the scripts as well. Example directory structure:
Code:
C:\USERS\***\DESKTOP\MABI
│ mabipatch.bat
│ mabiver.exe
│ version.dat
│
└───60
│ 58_to_60.0
│ 58_to_60.1
│ 58_to_60.2
│ 58_to_60.3
│ 58_to_60.4
│ 58_to_60.5
│ 58_to_60.6
│ 58_to_60.7
│ 58_to_60.8
│ 58_to_60.txt
│
└───patch
58_to_60.zip
Then just run the script and the process should be remotely painless.
Bash script for Linux - Requires Info-ZIP's zip and unzip. Requires diff and md5sum for verification (standard).
BATCH script for Windows - Requires 7zip. Currently does not verify patch pieces. (Click download and save as mabipatch.bat)
For those of you that don't understand command line principles (all of you), open cmd, cd to the work directory, and request help of the command.
That is on Windows: Windows Key+R -> cmd -> cd "C:\path\to\workdir\yes\this\is\an\example" -> mabipatch /?
/? is the standard help parameter for a command on windows. On linux it's --help but if you're on linux and you didn't know that you should go back to windows.
In before virus/account theft accusations! lol