Is paper reviewing for journals that are not JCR-listed worth the time? Is it worthwhile to spend some time as reviewer of journals which are not JCR-indexed? I do not know in the rest of the world, but in Spain all that matters are those listed in JCR.  

NOTE: I am a robotics PhD student yet, and I probably should focus on my research now.
My general answer would be yes. Doing reviews provides several benefits, first, you will see manuscripts before they are published. You will spend time reading new research in detail in a way you probably would not otherwise. You can use the experience to learn about how to write (or how not to write) a manuscript. You will contribute to your field as is expected from all scientists. Being appointed to review also signals someone has identified you as a possible expert in the field.

There are, however, some possible caveats. You should not spend time on manuscripts from disreputable journals. One way to gain insight into this is to ask your advisor about the journal if you do not feel you have the insight yourself. If the manuscript is far removed from your own work, you should probably also decline with the comment that it is not within your expertise. 

It is true that this will take time off from your PhD work to some extent but you will be able to learn from the experience if you consider the process of evaluating work and assessing the standard in which manuscripts are submitted. Of course, one review, will not give you all insights, but given that you do a few during your PhD time, you will gain new insights into the publishing world other than submitting and revising your own work.

A final point: reviewing for a JCR journal or a journal that is not listed should not differ. The review work is equally important for all publications. A journal that is not listed can become listed if published work is of high quality and thereby referenced sufficiently.