Often we'll get somebody with horrible latency on the input thread and when we troubleshoot the issue with them, it seems that at this point in development, the input latency (sometimes in acute episodes, sometimes sustained) seems to always be due to something external that hooks into our multi-threaded input thread. (Unless we are talking about really low spec systems.) We are talking about any kind of software that hooks into the game process intrusively either to show some information, to record some information or for security purposes, that has some bug making them block excessively during this hooking instead of releasing quickly. Note that not all software that follows this pattern causes issues, just some of them.
One that came up recently was that Comodo has an advanced "active protection" detection mode that is a bit more intrusive than the normal one that was causing this, once this user disabled this advanced mode and left just the antivirus running the latency became instantly good. The version of Comodo where we saw this was 22.214.171.12418. It may be that this is fixed in new versions of Comodo, so do not assume that you need to stay away from Comodo or this kind of setting because of this in general.
Now, we have a short list of some things that have caused issues (apps and drivers) where removing them made the latency issue go away, but it is a tricky subject. I don't want to say "X app" will ruin your input and contribute to giving these apps a certain reputation that may be undeserved, because they may be able to fix this pretty soon for all we know, these things have a way to stick in gaming for a long time. We do have unusual runtime requirements due to our multi-threaded input feature, and it's understandable that there are a few apps out there still doing things incorrectly and getting away with it, because the delay they are creating wouldn't be noticeable in non-concurrent input games that poll input at a very low frequency.
So to sum up:
For input delay issues, suspect anything that hooks into or interacts with the game process somehow. Turn anything belonging to that category off to start with and see if that fixes it, then turn them back one by one to locate the problem, and if you locate it we'd love to know. Diabotical with multi-threaded input On requires a clean, well-functioning OS environment much more so than other games. (This is another reason why MT Off is still there as an option).
We are hesitant to publish a full list of apps that have contributed to problems before we give them a chance to fix these issues, this is an ongoing process. Let's come up with an arbitrary deadline now for them to get back to us and say they'll look into it: October 10th.
If the process above doesn't go anywhere with some of the offending apps we can start detecting these apps when the game starts and give the users a warning once that they can dismiss, we will also put the list somewhere.