This was the first episode of The X Files that I had ever seen, and it got me hooked into one of my favorite series in television history. The story reverberated with me, perhaps due to my beliefs in the somewhat "Eastern" philosophies of reincarnation and bonded souls. That is why it came as such a surprise to me to see this episode rated so poorly. Two of the major themes that I see in the user comments are the perception of poor writing (personal taste, I guess) and the unrealistic portrayal of the hypnosis sessions.
Although I have not seen this specifically stated anywhere, I have no doubt that the inspiration for this episode comes from the book "Many Lives, Many Masters" by Dr. Brian L. Weiss, a psychotherapist who wrote about his experiences using past-life regression. The hypnotherapy scenes are extremely close to the descriptions given by the book, including the ability of the regressee to recognize "current" souls in the past, and the noticeable changes in demeanor and mannerisms as the regressee moves from identity to identity.
This episode is not for everyone, and I can see how fans may not have appreciated it as much as I did. I still consider it my favorite episode, specifically because it went beyond the odd, beyond the quirky, beyond the "are they out there or not." Instead, it was an episode more focused on philosophy and the meaning of life. A little heavy for a television show, perhaps, but outstanding for long discussions over a few drinks.
Oh, and for those who found this episode as entertaining as I did, I highly suggest the book "Many Lives, Many Masters."