Can I use JoomSEF for multiple domains?

The license is per-site (Joomla installation) regardless number of domains that are pointing to it.
If you have multiple domains pointing to a single Joomla site, you are fine with 1 license. In such case, specify the "primary" domain that you use to access the site backend.

If you have multiple domains and each of them is a separate Joomla installation, then you should have a separate license for each of the sites.