Console Tweaks
Thresh
Well, consider what you say. While I'm not personally against using such client-side commands (Quake II really puts the smack down on the number of options that can be toggled from the console), I think that they certainly do let you see more of what you're supposed to. Gl_modulate was first used because some 3D accelerators were too dark in Q2. Now, they're used to almost completely remove shadows and make entities brighter and more visible. While it's mostly sanctioned for use in the US, a lot of people have problems with modulate (after all, if it's legal, why isn't r_fullbright?), and rightly so.
Regarding polyblend, if you get pimped by a rocket to the head, your view is supposed to jitter and the screen is supposed to flash red. Consider an old-school example. In Doom, a good shot caused a red-out that was so severe it completely blinded you. Take that out, and you've just removed a key element of the game! Also, FOV (field of view) increases what you can see peripherally - should that be considered fair?
Kenn
Hold on there! For one, that wasn't something in Doom you could easily adjust (at least without the help of an external program, though I do remember a bug allowing you to reset palette shifts in-game). Also, in Quake, the importance of the palette shift was greatly diminished by the introduction of GLQuake - that setting became a console command just like any other.
Thresh
Well, from there, it all goes back again to whether or not you consider console tweaks cheating! Personally, I think all console commands are okay to use. As long as the console commands are accessible to everyone and is shipped with the game, it should be free to use. Course, if GL console commands are kosher, what happens to all those disadvantaged because they don't have a 3D accelerator card? This problem spawned the entire "waterhack" and "untextured DM3" debate. Waterhack was a program for Quake 1 that modified a level (specifically DM3 for team games) by removing the water texture, allowing players to see through it (similar to using r_wateralpha in GLQuake). You really couldn't consider that cheating unless you also considered the gl_polyblend or wateralpha commands cheats as well.
Kenn
Well for your information, an untextured (or differently textured) map serves the same purpose "mipcap," a function available on non-accelerated Q/Q2 that can greatly reduce texture detail and also help speed up game performance. Unfortunately, the untextured map also makes it easier to see enemy players, which once again opens the door for debate.
So what are we left with then? Aliases? Key bindings? They're essentially console tweaks as well. I've seen people who claim rocket-jump aliases are cheats, or fast-weapon toggling (binding specific keys not only to change weapons, but to fire them on the fly). There's also a controversial little alias that switches your weapon to the shotgun after you fire, making it difficult for the enemy to get a weapon from you if you are killed. While I say "more power to them," a lot of people are going to ask "where does it stop? What can we as gamers do about this?"