Where is Eren's father Dr. Jaeger?
The whereabouts of Dr. Jaeger are revealed in chapter 62. To give you an idea how far ahead that is, the latest episode (25) plays out during chapter 33, so you are basically halfway through.


   Eren has eaten his own father. This event happened somewhere during the time-skip of the second chapter, so Dr. Jaeger has basically been dead for most of the series.