I thought about this hard enough I took a shower to think on it, but if I sat down and wrote out all the stupid shit I saw 10 years ago it would take many pages of this thread up for what would just amount to a collection of a few laughs, with no real lessons taught.
Instead I think what is probably better is to tell you what I would do differently if given the chance to run something like that again, and let your imaginations fill out the gaps as to why.
When running a 40+ person west marches servers you will usually have about 15-25 active members at a time and I think over the life of that server about 70 people passed through. When you have that kind of volume you must get a few people to GM in addition to yourself. I was running 3-5 games a week at 3-4 hours a game in addition to a full time job. I had 3 people who were supposed to also run games but usually only ran 1-2 games a week, if that. I also, as mentioned, was playing pathfinder 1e and anyone who has played it knows the game has pretty shit balance. As such I took it upon myself to fix the game via houserules because there was a reasonable amount of doubt about OP shit. These houserules would get run by the other GMs to kind of poke holes in them to feel out if they were bad or good before they were implemented. Which brings us to our rules.
1) You are the only real Human in any online tabletop group. They aren't people, they just sound like people. Their opinions are retarded and the chances you are speaking to a pedophile piss-fetishist are never 0%. Treat them how they deserve based on this information. No offense to you guys, but you couldn't waterboard me to change this opinion.
2) Given the above if you decide to run one of these God forsaken hellholes you MUST rule with an iron fist. You should larp as the most brutal dictator in history. If you even suspect someone of being a freak or degenerate, of stirring shit behind the scenes or if they so much as crack a joke about anything you say you ban them instantly without even a note. You have 40 retards on hand to step into their shoes, they won't be missed.
3) Never pick a d20 system for a group this large. Roughly 15-25% of the online tabletop community are cheaters. I would say about 12% of them do it deliberately but some of them are just really dumb and extremely bad at keeping a character sheet that is up to date. Reduce your bookkeeping at every possible juncture unless you like doing professional accounting for free.
4) To add to the above, the system should have a character sheet that can fit on a notecard. Anything more is not worth the effort.
5) Furthermore don't run systems with RNG levelling elements, like rolling HP at each level or rolling for stats at the start. If you do you will have to make them roll-averaged and point-buy respectively anyways.
6) No Canadians.
6.1) No Troons.
6.2) No Furries
7) Interview everyone who wants to join, but require facecam during the interview. Freaks recoil from showing their face like a vampire to daylight. Also lets you check their room for filth.

Be harsh but fair. Let the dice roll in public always so nobody can say you fudge one way or another. Let them know they died because they are a traumatic brain injury victim, not because you were "out to get them".
9) Get a good VTT, not roll20. Foundry is decent.
10) Force people to post their before and afters of their character sheets in a specific chat for record keeping.
11) Expect to be paid by the people who want this. I wouldn't ever do this again for less than 150k/yr. Open a form of buy me a coffee or something. I ran games 20 hours a week. I RAN them for that time. You do the math on how long I spent doing prep work. I had a 40hr a week job I had to take public transit to and from during this time too.
12) I really cannot harp enough on how important a lightweight system is for this. You want mechanical depth, but not on the character sheet or monster blocks. Nothing comes to mind for me and I have played a lot of games since then.
13) If someone fails to show up just go on without them. If they show up mid session tell them to try again next time. If they have any further issues see rule 2.
14) You will have to get good at generating dungeons and quests as you go about your day. Use a notepad app on your phone, a google doc or something, but write down your thoughts constantly or you will get so behind you never catch up.
15) When in doubt run adventure modules if you can find them. Lots of people have never played any of Keep on the Borderlands or other great classics so you are free to use those old modules and nobody will know the difference.
16) MinMaxers are actually your best friends. They know the system inside and out, they understand damage curves and stat averages. Most of them are honestly chill people and are happy to tune it back if you need them to. The best ones you can even ask them to tune it back a specific damage per round and they will immediately know how to do it. Use them as resources for if you need to solve a problem on your end as a GM and let them help people who are lost and don't know what they are doing.
17) Meta Gamers are not your best friends, especially ones keen to hold a grudge after playing like a fucktard.
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If you get GMs to run games for you be sure to randomly drop in mid session for checkups. Remember rule 2.
19) Figure out a guideline for XP and wealth distribution for dungeons that GMs can use to run things smoothly. 3.x having wealth by level does help this some. This is as much for your sanity as for anyone else's.
20) If you want to implement a houserule ask around online to see if anyone has anything intelligent to add then do whatever you want anyways. The opinions of others are worth nothing and you probably know better in any case. Remember that for someone to impact your decisions you must first respect them as a person, see rule 1. Learn to ignore other people and make your own decisions, but feel free to collect ideas you might think are novel in some way. Only you can see your vision of the game you want to run or play and so only you can make that happen. Also don't feel bad when a rule doesn't work out, get back on the horse and try it again.
21) To be honest, don't run a 40+ player server.