For individual words, I left markup tags in the translation lines for the reasons stated in the comments above. If you select blocks of text, whole sentences, numbers, etc., I would put it in the template, if possible, since this is not exactly what you would have to confuse with the translation.
A good idea might be a flag in a template that you made using comments. You will also need some reliable process so that all translation files are changed if you decide to change the emphasis ever (which you will inevitably be). This is a pain, so I try to avoid adding emphasis to individual words, where possible :)
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