I finally found a solution for the most annoying linux problem I had for years! TL;DR: System is now far more responsible during disk I/O with the lowlatency kernel, source: https://bugs.launchpad.net/ubuntu/+source/linux-source-2.6.22/+bug/131094/comments/390
I have a linux box (waxford) that is used as a home server for all my needs at home (media, file server, dev server, backup, ...) but also as an always on desktop. It's an old (by current standards) AMD 4450e with 2x2.3Ghz and 3GB RAM and a (software) RAID5. If I remember correctly, I installed it as an Ubuntu 08.04 server and upgraded up to 12.04 over time.
The problem was, that after one of the updates the machine was unusable as soon as some disk I/O happened. Playing MP3s while running updatedb, installing updates or starting Thunderbird was impossible and the mouse would stand still for seconds. Very annoying and embarrassing.
Yesterday I read a comment in the bug report for that problem, which I'm subscribed to for years as well, with a possible solution. As described there I switched from the server kernel to the lowlatency kernel. That surely brings some throughput penalties in benchmarks, but in real live usage my machine is usable again. It doesn't feel sluggish all. I'm really happy about that simple solution.
The bug existed since 2007 and still isn't officially closed. In the roughly 13 years of using linux little annoyed me as this did. I had to fight with so many drivers and incomplete implementations of stuff - after all its free software, I'm free to extend or not to use it. But this drove me crazy, in a lot of ways my linux desktop in e.g. 2004 was far more usable than my way more powerful machine during the the last few years.