I haven't seen usage statistics but for what it's worth (non-quantitative but a personal view) there are several you can probably trust to stay around if you have a look at who's behind them...
My favourite is Jade by visionmedia / TJ Holowaychuk - the same guy behind Express. EJS is more 'traditional' and also a visionmedia project.
I seriously doubt these are rarely used or in danger of dying out if you look at the support they have (popularity of github projects, plugins for IDEs, etc)
Swig also seems very good and broadly used, based on the very popular django templates syntax...
The other suggestion I have is that some template engines support similar syntax and features (e.g. Jade is similar to HAML, Swig is a port of Django templates, Handlebars uses the same syntax as Mustache, etc.) so you could pick a popular syntax and, if your engine of choice falls behind in the future, there may be a compatible alternative you can switch to without too much trouble.
Finally there's a good list here -
http://paularmstrong.github.io/node-templates/ - by Paul Armstrong, who's behind the swig project.
Hope this helps.