For any purpose, JC1 as a mean to study mitochondrial energization should be the last reserve. Without knowing what you exactly want you exactly plan to study, it is difficult to give any advise. JC1 is too touchy, too many complications in the usage, therefore information is full of doubts.
I completely agree with Alexander. For instance, JC-1 is not regarded as a reliable way to measure the mitochondrial membrane potential. You can find an interesting discussion on this topic here:
"Mitochondrial Biology: New Perspectives: Novartis Foundation Symposium 287",
edited by Derek J. Chadwick and Jamie Goode (2007)
Is it difficult to say what is recommended, but we used Mito Tracker Orange in bovine oocytes before and after maturation and it was very good. More sensitive than R123 or Mito Tracker Green and for localization is it very good fluorescent dye.
Many thanks michal, I saw your published article in 2012 " Characteristics of bovine oocytes with different meiotic competence...". If you have other articles related to this subject I do appreciate if you send it to me.