I kept having this issue. This helped me even thought it still sometimes jumps to 100%. Hope it helps!

id switch to windows 7. that 100% disk usage must be wut windows 8 thinks is "making the most of your pc". Idk if this has anything to do with it at all but does it start when your playing a game that has custom aspect ratio? this is used to cause high disk usage usage for me...then i went to windows 7. now it just warns me about high disk usage but it fixes itself in a matter of seconds

Windows 7 will not fix the problem (at least, not uniquely). I have had a similar problem and one of the causes can be prefetching; the system tries to load processes you use often into the RAM, causing the disk usage to spike. This guide details how to disable superfetch and prefetch; in this case on an SSD but the instructions should work on an HDD. This guide only deals with superfetch, but I believe disabling superfetch alone should solve the problem. I would only use the registry edits in the first guide if shutting down the service doesn't work.

I've had the same issue with Windows 8.1 and I've solved it. The thing is, you have to tinker with the Paging File Size.
Here is a link.
Depending on your RAM and HDD space, you might want to increase it or make sure you let it stay at automatic.
Just play with the settings a bit and you'll get it solved. I worked for me so hopefully it'll work the same for you, Sam.

Windows 8 monitors disk health and will defrag and attempt repairs in the background, it is more proactive compared to previous iterations of the OS. If you're stuck constantly accessing the disk all the time this suggests something may be wrong with your hard drive; you want to do a full disk check and surface scan, as this can take an age, you are better off leaving it to run over night.

With 16 gig of memory the page file is not the source of the problem, likewise superfetch should not cause excessive drive load.

To those people saying to go to Windows 7: shut up. It's neither clever nor helpful.

So in the interest of countering the spread of this disinformation circlejerk: Windows 8 is not that bad. Yes, out of the box the OS is a step back. But with a third party start menu solution W8 becomes a perfectly usable solution. In fact for certain features it's an advancement over W7. It boots hella fast, the task manager is a huge step forward, and its tablet functionality is superior to W7's. The metro interface and MS cloud features can be bypassed entirely. Granted I cannot tell you how it affects gaming performance since my W8 device is a tablet, but so far W8 has been compatible with every program I threw it at it.

Windows 8 is functional. More functional than Vista was at launch. It shouldn't be misrepresented as a disaster.

Next, to OP's problem. When did you start to notice what was happening? Check your background processes an event viewer for anything out of place. You can try 'view reliability history' (I don't know how you would navigage to it without a start menu program). If you can't find anything there, try using system restore to restore the system to a date before your disk usage problem started occuring and then systematically search for the culprit. Make sure your OS and antivirus are up to date and not compromised. It might help to unplug the machine from your network if you suspect that it's been infected.

I had the same issue on my laptop and, not only was windows 8 being stupid but, my HDD was dying (I have no idea if this was windows 8 related in any way). You might want to check your HDD's health using something like CrystalDiskInfo or, your manufacturer's tools (like Western Digutal's Data Lifeguard Diagnostic for Windows).

Now I'm on windows 7 and with a working HDD and, I'm quite happy.

USE LINUX!

It happened to me once and it was because Box Sync. Maybe you have some software similar to this?

This is a Bug go back to win7