(In progress. Last Updated 2022-12-10.)

I spent a fair amount of time working on my Discord Server to make it secure, functional, and fun.
Here's a general guide to how I have mine setup.
Hopefully you'll find something in here beneficial for your own setup.

1. Remove all permissions from Everyone role. (I also explicitly deny Everyone the View Channel permission on every channel)
   
2. Create a basic role with appropriate default permissions.
   
   • You'll need to manually add an appropriate role to Bots you add. I have a Bots role I use for them to separate them from normal users.
3. Add the basic role permissions to the appropriate public channels. (I explicitly set the permissions on each channel category, but that's probably overkill)
   
4. Setup a Rules channel and give Everyone role View Channel and View Message History permissions.
   
5. Setup a Rules message with a reaction role to accept the rules and get the basic permissions role.)
   
   • I use Mee6 to setup my reaction roles. If you only need a couple Tatsu has a very nice reaction role creator in the free version. YAGPDB can do them as well but it's a bit complicated.

If you are doing this on an existing server, you should probably add the new role to your existing users before locking down the Everyone role, unless you want to force them to all accept the new rules.

• Mee6 (Premium)
  1. Welcome and Goodbye Messages
  2. Custom Commands
  3. Reaction Roles
  4. Audit Logging
  5. Channel Content Restrictions
  6. Searching
  7. Voice Recording
  8. Timed Messages
  9. Statistics Channels
  10. Temporary Voice Channels
  11. Stream/Social Media Alerts
  12. Levels (silent)
• Beemo
  1. Bot Raid Protection
• BibleBot
  1. Bible Verses
• Birthday Bot
  1. Cross Server Birthday Notifications
• Chat To Twitch
  1. Discord/Twitch Crosschat (not quite stable yet)
• Counting
  1. Counting Game
• Dwemer Automaton
  1. ESO Notifications
• GamesROB
  1. Social Games (haven't played with it much yet)
• IdleRPG
  1. RPG
• PatchBot
  1. Free Game Notifications
  2. Game Update Notifications
• Tatsu
  1. Levels
  2. Pets
  3. Housing
  4. Fishing
  5. Other similar stuff I haven't messed with.
• YAGPDB
  1. Automod
  2. Logging