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Some things I've thought about:
The good thing is the link to my site. But after that it becomes less clear.
1) What is the nature of the site linking to you? If it's a spammy site the link may do more harm than good.
2) Many sites using templates won't have much PR value, so even if many sites use the template, it will not be of much value
3) Semantics and reach. It's better to have a site with more or less a similar topic linking to you. So that would mean adjusting the template a bit to encourage only similar sites to use the template. This can be done through a header image or so. The disadvantage of this is that your market becomes much smaller than when you would adjust the template to have as much reach as possible.
Any thoughts on this?
The link from your template will have the same anchor text on all the websites that use it, therefore the link will be easily recognised by the SE's as one that is not natural.
(natural links from hundreds or thousands of websites will vary in anchor text)
Links from Websites that are inline with your topic will definitely be of more value.