For grates, you can use textures with alpha channel, commonly referred to as fence textures. Not sure about glass. You should study maps that use the things you wanna do. 

for glass, you add the brushes to a func_wall entity and set the key "_alpha" "0.5" (or adjust as needed) 

InsideQC was actually the first place I checked, but the Tutorials are gone and nothing in the corresponding forum, didn't think about the WayBackMachine.

Based on your tutorial, I added an extra spawnflag for silent spawning and maybe I'll add the functionality to the item code as well. Seems this is the only sensible way of tackling my problem at hand as all other attempts have been fruitless. I also thought about throwing in the corpse removal code for some extra edicts if needed, but I'm currently stuck at trying to make it optional, to be enabled through an impulse command. Minimal QC skills... 

Thank you for the info! I appreciate it. 

Although you could make a way doing impulse commands ... just using one of the existing single player cvars would be easier (temp1, saved1, saved2, saved3, etc.)

if (cvar ("temp1") == 0)
{
// Dead body removal not wanted.
}
else
{
// Remove dead bodies
} 

I Tried the key "_alpha" but didn't seem to work
"alpha" without the underscore does seem to work though :) 

Firstly it's important to remember that it's a feature added in custom engines. Almost every engine these days supports it, but not the originals. alpha without the underscore is correct, but in most engines you need a mod which includes it or it won't work. So loading the map in e.g. Arcane Dimension or Quoth the entity will be transparent, but in standard id1 quake it won't be.

If you're writing your own mod, adding support is really simple, just add

.float alpha;

to the bottom of defs.qc 

alpha works just fine in id1, as evidenced by skacky's jam2 map. 

In e.g. darkplaces the waterfalls are opaque, it depends how each one handles it. Some engines fail to load the key if it's not in the progs definition. 

fitzquake-based engines should all support it without mod support 

I started to wonder if there's some modified ID1 progs.dat with alpha added floating around. 

Preach is right, but the sand has shifted. Around the Quoth 2.1 days, every engine required a .alpha field or nothing would happen.

After FitzQuake 0.85, any engine without automatic .alpha support would get users complaining -- and it is universally supported in modern times (qbism, requiem, qrack, fte, etc.)

DarkPlaces has automatic .alpha and has had it not too long after Fitz 0.85, but sometimes DarkPlaces draw is not the same due to fog or skybox or depth sorting or draw order or even lighting.

[One time I thought DarkPlaces was ignoring .alpha -- it wasn't --- magnifying a screenshot showed it was transparent but the draw blended differently with the background and it was hard to notice.] 

Ah yes. Worth a try. 

Do messages from trigger_once and trigger_multiple entities have to have a sound? I'd like to make it silent but the 'sound' value 0 (which is listed as 'silent' in Trenchbroom) still causes the normal beep-boop message sound to play. 

If a message is displayed, I think it's better to leave the beep on: sometimes in the heat of battle a centerprint can go unnoticed, the beep is useful then. 

"sound" ""
maybe? 

The QuakeC looks like this:

void ()
trigger_multiple =
{

if (self.sounds == 1)
precache_noise ("misc/secret.wav");
else if (self.sounds == 2)
precache_noise ("misc/talk.wav");
else if (self.sounds == 3)
precache_noise ("misc/trigger1.wav");

if (!self.wait)
self.wait = 0.2;

...
}

"sounds" "0" // <---- notice this is plural

Would seem to work. 

Unfortunately doesn't work; I made a typo in #18793 and the default included field is actually sounds, with an s at the end. It does list 0 as 'silent' (http://i.imgur.com/knuXpZT.png) but after a bit of fiddling, apparently the sounds field is only for activating the trigger itself- leave the sounds field blank and the trigger will be silent, set it to 1, 2 or 3 and you'll get the respective secret, bleep-boop or mechanical clunk sounds. It's only when you include a message with the trigger that it forces it to play the bleep-boop even when set to silent. 

Might have to edit the QuakeC in order to do such a thing then. 

The talk sound doesn't play if you set a sound on the trigger! So what you can do is leave "sounds" at "0", then explicitly set "noise" "misc/null.wav". That way touching the trigger plays a silent sound, and the talk sound is suppressed.

Note that you will need an entity somewhere in the map that precaches the misc/null.wav sound, like a door or platform with "sounds" "0", otherwise you'll get a error message. 

What's the best way to work around the MAX_PATCHES?

I consistently hit it even though my maps aren't that big or detailed. I know it's related to the lighting quality and the size of the map, but I just wonder how far you can go and what to sacrifice etc. for a larger map to be possible. I'm all about huge and impressive maps, but I also want them to be lit too. 

The default patch size in the original utils is 64 units, try raising it a bit with "-chop 70". This will make the radiosity lighting a bit lower quality.

It should be possible to raise the limit in the light tool, the patches only exist during lighting so it won't affect engine limits. (but the more patches there are, the slower the light tool will be).

#define MAX_PATCHES 65000 // larger will cause 32 bit overflows
I'm not sure what overflows though. 

I use quality 128 for sky and 256 for water.

How would I raise the limit during the light tooling? 

Raising the limit would involve changing that #define and recompiling the light tool (and check if it breaks anything in the tools :). http://github.com/id-software/quake-2-tools

I use quality 128 for sky and 256 for water.
How about regular solid faces? The vanilla tool only seems to have one -chop option for all faces. 

I use the Arghrad.