How to limit HDD write speed for chosen programs

Unfortunately, you can't do that. Hardware is abstracted from applications and even parts of the OS. In essence, the application says "write this to disk" and the OS handles it. The application doesn't handle how or even when it gets written. All of this is handled at the driver and kernel level and there is no real way to change this.

Even if you could do this, the fact is you are using a spinning magnetic disk - and a very slow one at that - you wouldn't see much gain. The drive is constantly spinning and the heads are moving along the disk. Even if you wrote to your file less, the disk will constantly be seeking the right areas on the disk to read/write to/from.

Your best option would be to get another drive and do your work on that drive, leaving your first drive for your internet, MP3s, etc.

P.S. You didn't mention how much RAM you have. Swapping could be a factor in the slow speed. Depending on how much RAM you have, adding more will only help.

Process Lasso allows you to prioritize I/O. From their FAQ:

New in v4.1 (v4.09 beta), Process Lasso has explicit current and default I/O priority settings available those who require them. This only applies to NT6+ (Vista,Win7,...).

HOWEVER, Vista's I/O prioritization is based on the priority of the thread doing the I/O, which is dependent on the priority class of the process doing the I/O. There are actually only two levels of priority usable by applications, Normal and Very Low. Although there are technically 5, only these two are implemented or usable by processes.

Therefore, adjustment of the thread priorities will propagate to the I/O of that thread. In this way, Process Lasso already does I/O prioritization. Microsoft recommends applications adjust their I/O priority based by setting the calling thread's priority (directly or by adjustment of the process priority base class).

See also the paper on I/O prioritization from Microsoft.

What I do when I have a process that keeps eating all my disk I/O on Windows is bringing up Process Explorer and pausing the offending process. After I'm done with my business and am ready to wait a bit I resume it. It's definitely not the most productive way of doing it since it's all-or-nothing way of controlling disk I/O and your process will have to wait while you use your computer, but so far I haven't seen any better alternative.

On the other hand, if you can do your process on Cygwin, you can install pv on your computer and use it as the first or final step with an option (I think it's -r) to throttle pv's output rate.