Here is something which annoys me for quite a while, probably some people don't even know it so far:

If you edit any post in a thread, the entire thread is “bumped”, this means the thread will rise to the top in the thread list (I ignore sticky threads in this example), as if a new post has been added.

This is sometimes useful, but most of the time annoying. You can't just fix small typos or fix a broken link without bumping an entire thread.

So I suggest this:

Add a checkbox in the post submission form, saying “Bump the thread” (or something like that, this may not the best text) and it is off by default.
The thread should only be bumped when this checkbox was ticked.

I hope this would reduce the number of unintentional thread bumps a lot.