You can create up to 100 tracking IDs on your associate dashboard.
At least use a different ID for each site so you know which site is delivering the most results.

If you're doing PPC you want one ID per keyword

If not, then it depends how much you want to analyse your visitor clicks.

For example:

Lets say you want to nail it down, and have 5 Amz contextual links on a page, then you have three big, bold calls to action at the top, middle and bottom of the content and you also have 5 images.
By giving each link a unique ID you can track exactly what and where you visitors are clicking.
This data can be valuable, it can give you a good idea of what works and where it does, for a particular site, you don't need to do this on every page of course.

Also different sites may have different user behavior, but you can use data gathered as a starting point, and tweak from there.

For speed you can also use one unique link per page, or you can separate text and image links, there are many variations.

If you run out of ID's you can just contact Amz and ask for another bunch.

Another good reason for using a different ID per site is that it will prevent anyone discovering your sites (and niches)

Yep, I definitely already do this.

This is a good idea.

To test I am taking the most popular page on one of my websites, and created three new tracking ID's to test the CTA, text and image links.

I don't know why I didn't think of this before, I suppose I just thought I needed to track every single link individually, when it's probably better to just see which links and where convert the best in general.

Thanks.