You can't, the templates are not linked to the projects in any usable way.
The best you can do is detect the project and do conditional formatting, like:
##common header stuff
#if project 1
Output stuff for project 1
#if project 2
Output stuff for project 2
##common footer stuff
JIRA can't out of the box, as Nic says, for small tweaks, a range of small changes can be combined into one particular template, but if you want more than that, its going to be quite hard to manage.
Another answer to the question is that JEMH (plugin) can be used to do exactly that, to provide a completely different set of runtime modifiable templates per project. In effect, JEMH takes over the notifications, so you would deselect the JIRA notification scheme in the project and select it through JEMH instead, associating the per-event templates you want.
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