People behind qoto.org have customised their Mastodon instance, and added a tons of great features.
Here are the best ones in my opinion:
‣ Inline math Latex support
‣ Full text searches
‣ Groups Support - Accounts which represent groups are now tagged with a group badge and are specially rendered so the messages relayed by a group appear to be originating from the user.
‣ Markdown Posts - You now have the option to select markdown formatting when posting.
‣ Circles - You can now create circles with followers in it. When you make a post you can select one or more circles to privately post to and only users of those circles can see your post.
‣ Per-toot option allowing for local-only toots that wont federate with other servers
‣ Domain Subscriptions - Bring another instance's local timeline as a feed in Qoto, no need to have an account on another server again, just import their timeline here!
‣ User Post Notification - Users now have a bell next to their name where the follow button is. This will send you a notification every time they makes a new post.
‣ Keyword Subscriptions - Create custom timelines based off keywords not just hashtags, you can even use regex for advanced matching
‣ Read/unread notifications - Unread notifications now have a subtle blue indicator. There is also a “mark all as red” button added.
The only downside is that they are running on an old version of Mastodon (v3.2.1), but I imagine it's much harder to update when you have that many customizations implemented.