Quake was intented to be very customizable and easy to edit or even to make a new game out of it. Therefore there are many ways to cheat by editing certain files. There are 8 types of files I will show how to edit, namely *.mdl ; *.bsp ; *.pcx ; *.spr ; *.wad ; *.wav, *.pak and *.exe
It would be easy to make all those cheats impossible, by using a crc check for all bsps, mdls and wavs, but like that every connect would take some more time.
You may download all of my changed files in the download section.

PAK:

The most easy to edit and also most used filetype is the pak-file. It´s just used to store all other files quake needs, like a zip, but it doesnt zip the files. To open, extract from and copy into a pak I use a program called Pak Explorer which looks like and also works like the windows-explorer. You may of course use any program you want.
If you make an additional pak in your id1 directory you have to call it pak2.pak, the next must be called pak3.pak and so on. Quake won´t read your paks if they are called else.

PCX:

The pcx-file is simply a picture, wich Quake generates or uses, for example a screenshot. The skins for Quakeworld (in quake\qw\skins) and those used for models in qme (see mdl) are also in pcx format. To edit those skins you need a paint-program, I would suggest Paint Shop Pro for this job, but you can use whatever you like. Quake only supports 256 colors, you may download the palette here. As a base for making skins the base.pcx in the skindirectory is just right. But before editing a skin you should know what sort of skin you want to have. For Free For All I would suggest a skin which shows the pants and shirt color of the player, so that you know whom you gibbed. The 2nd row of the palette is for shirt and the 7th row for pants color, the rest of the skin should have one of the bright colors at the bottom, so that you see the enemy quickly and even in the dark. An example of such a skin is here. For 1on1s and teamplay a skin which is totally bright colored is better, like this one. And as a skin for your teammates a red, yellow or even a dark skin is good, so that you don´t accidently shoot them. Here is the skin I use for teammates, just rename it to your clanskin.
To use those skins in QW the best idea would be to rename the base skin and delete or move all other skins you have. Then disable downloading by using "noskins 2" and set the baseskin you want by typing "baseskin <skinname>" in the console and then typing "skins" so that all skins are refreshed. For teamgames either everyone of your team has to set to your clanskin or you have to use a proxy for skinforcing, so that everybody in your team has your teamskin and all enemys have the bright skin.

SPR:

spr stands for sprite. Quake uses only 3 sprites, the bubbles when droning, the gold ball light and explosions. In my opinion the explosions sometimes block you sight, so that I just deleted them. This is done with Adquedit, a very good editing program for Quake. You just have to extract "s_explod.spr" from pak0.pak in progs and open it with Adquedit. Then you edit it with Paint Shop Pro and delete the explosion effect from all 6 frames. The file should then be placed in pak2.pak, so that you can still use the original sprite if you change your mind.

WAD:

A wad in Quake unlike in Doom is the file where the font for Console and Statusbar is saved. The reason to edit the font is for example to give the numbers another color so that you see better how many health, ammunition and Armor you have to change look, color and position of the crosshair, because in Netquake it isn´t in the middle of the screen, QW fixed this, or just to make your Screen look better.
If you don´t believe the crosshair bug in netquake look at these 2 pictures. To make the crosshair a bit more accurate I moved it as far left and top as it´s possible in the gfx.wad, but it still isn´t in the center. For Quakeworld I used the commands "crossx" and "crossy", so that even the moved crosshair is still in the center in Quakeworld.
A very good program to edit wads is again Adquedit. After extracting gfx.wad from pak0.pak open it with Adquedit. You may extract and edit the font with Paint Shop Pro then and after finishing it you should also put it in pak2.pak.
What I also did was marking my name with a blue box by replacing one of the characters, so I can see with a short look if it was me who gibbed the enemy or if it was someone else of my clan. It can only be seen by me, other players see it as the normal character. Other people (like the clan DeathRow) use numbers in their names to accomplish this, but its much easier and better to see like that.  I won´t tell you how it works exactly and it´s not included in the downloadable paks, because if everybody uses "my" character then I will see every name with the blue box, which is the last thing I want to happen. But it´s easy to figure it out yourself, especially if you execute this file in Quake, which shows all the possible ascii characters and their number.

WAV:

Quake´s sounds are stored in wav´s, which can be found in pak0.pak and pak1.pak in the directory sound (strange (-: ). With Pakexplorer you may even play the sounds without extracting them. You may replace and change all the sounds, but because I got used to them I only changed some, or better deleted them. These sounds are the ambient sounds, for example the sound of a torch, which sometimes disturb. I just replaced all sounds in the ambience subdirectory with a silent wav. Like that all ambient sounds are gone, not just the nonpunczual ones you can disable with "ambient_level 0". Here is the sound I used.

BSP:

The bsp-files contain the infos for all quake maps, the textures, the entities and the brushes. Unfortunately you can´t change the brushes in a bsp-file, thats only possible in an uncompiled *.map file. But it´s still possible to edit the entities and textures by using Quark or Adquedit. Editing entities won´t get you anywhere because only the server uses them, but editing textures was quite popular before the release of QW 2.20. With the map CRC checking you must have the same map as the server, so you have to use the original ones (or those revised for transparent water since 2.21). But if you still play QW 2.10 or lower you might want to know what to do with those textures. The most important thing to do for every non-gl player is to waterhack the maps. This little tool deletes the texture of the water, so that you may see items and players in the water, like with the transparent water option of Glquake. To get waterhack to let you also see through teleporters, slime and lava, like in Glquake, you just have to change the texture names of the map before running waterhack on it. For example renaming the texture *teleport to *watertele will make waterhack think it is a water texture and therefore hack it. The same works with *lava1 to *waterlav and *slime0 to *waterslim. But you should keep a copy of the original maps, because this is irreversible, so you will never be able to play on a QW 2.30 server with these maps. I have an additional pak4.pak, which is renamed to pak4!.pak by my batchfile if I start QW 2.21 or higher, and will be renamed back to pak4.pak if I play Netquake or QW 2.10, so these maps aren´t crc checked.
Another thing which is stored in bsp format are some of the items, for example all ammunition boxes, the mega health and the health boxes. I modified my mega health, so that you can see it from far away, for example from the outside of the rl room in dm5 or from the nailgun in dm6. To do this I had to use unbsp (a beta, which works just for amall maps) on b_bh100.bsp, to get a map file from it, which I edited with Qoole, but Quark works too. I added some new brushes to the original brush, so the megahealth can be easyly seen. Then I compiled it and with another final step the modified mega health was ready. But this cheat is considered illegitimate, because you can see the megahealth through walls so I won´t tell you what to do. I just wrote about this to show how easy it is to create such a bsp.

MDL:

The mdl-files contain the informations for quakemodels, like the playermodel, or models for weapons, quad or even a grenade. This is the most used way of cheating, because it´s that easy to do and may have big effects. In my opinion the best program to edit mdls is Qme. You can edit 3 aspects of a model, it´s form, it´s skin and it´s properties. The most obvious thing to change is the skin, so that you see a rocket, a grenade or even a backpack much better. In Qme there are 2 important options, the skin texture editor, where you can paint like in any graphics program and the skin color editor where you can easily replace colors of your skin, an excellent feature.You may of course also extract the skin and use a graphic application on it, but you have to use the quake color palette. Changing the form is also easy, you just have to move the vertices in the frame editor or you may also add new geometric forms or delete vertices. And the easiest thing is to change the model properties in the model property editor.

I changed the following (all available in the download section):

For Netquake I also changed my player.mdl a bit, I replaced the skin by a bright one and removed the corpses by reducing the last frame of each dying sequence to a pixel (in QW you can filter them out by using a proxy). I also made the Quad glow, like in QW. I put those 2 models in my pak4.pak, which is only used for Netquake.

EXE:

Yes, it´s possible to edit the Quake executables (qwcl.exe, winquake.exe, glquake.exe...) using a hexeditor. But I won´t give you any details on how to do this, if you want to know what effects this has look in the illegitimate section.
The only thing I will talk about here is the polyblend remover by Kenzie. This little tool finally removes the biggest disadvantage of software Quake players, so that everybody may have a crystal clear view under water. Ruiner even improved the patch by also removing the powerup palette changes and by making it possible to set the intensity of the changes (get wbh here). Unfortunately this program only works with the windows executable and the "f_modified" option of qizmo and cheapo will show that the executable is hacked. The only way to get around this is to download the already hacked executables here (also for linux, all around 300kb). But those only remove the polyblend in liquids.
Seems like I have to tell some details about hexediting after all, because I found out some more hacks and have no idea how to write a patch. But note, that it´s illegal to modify the executable after paragraph 3a of the Limited use software license agreement. This is why I can´t post the already hacked executables here.
First you need a hexeditor, I am using UltraEdit-32 but any other will also do the job. Then you have to open the executable you want to hack and look in the table below what you have to modify. You have to replace the numbers in red colors by lower ones or use 00 to completely remove, but note that those intensity numbers are hex numbers, to convert them to decimal numbers you have to use the windows calculator in scientific mode (eg. AB=171).
 

if u want the Hex string's Email me and ill see is u are worthey
 

What is changed	Hex string	Adress (qwcl.exe)	Adress (winquake.exe)
for all the polyblend effects to work you have to change those to 00:	0000 0000 0000 0000 0000 0000	000000000 000000000 000000000	000000000 000000000 000000000
Water polyblend	0000 0000 0000 0000 0000 0000 0000 0000	000000000	000000000
Slime polyblend	0000 0000 0000 0000 0000 0000 0000 0000	000000000	000000000
Lava polyblend	0000 0000 0000 0000 0000 0000 0000 0000	000000000	000000000
Quad polyblend	0000 0000	000000000	000000000
Penta polyblend	0000 0000	000000000	000000000
Eyes polyblend	0000 0000	000000000	000000000
Biosuit polyblend	0000 0000	000000000	000000000
All of the above may also be changed by wbh
Pain flash (Better than the proxy removal, because the face in the statusbar still changes, and if you make this red like in Kenzie´s wad you will easily map dm3see when you are attacked)	0000 0000	000000000 +  000000800	000000000
Pickup flash	0000 0000	000000000	000000000
666 in status bar if you have pentagram is removed, so that you can see your armorvalue, like with nfproxy The yellow numbers change the 666, E703 would be 999 for example	0000 0000 0000 0000 0000 0000	000000000	000000000

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If you have Improvements to these files or have another idea of editing Quake´s files, please tell me
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