So my wife was on modafinil for a time, due to being very sleepy for unknown reasons. The doctors figured it was better than whatever stims they had her on before. Within a year or so of starting her on modafinil, they told her to discontinue use because there are indications that long-term regular use causes neurological damage.

I don't know what their sources were for that, and it seems likely the doctors would be very conservative in prescribing experimental drugs, so there was probably an abundance of caution in play there. That said, the long-term side effects really are not well understood at all, so I'd think twice before making a regular habit of modafinil use.