Up until a couple of weeks ago, I did them by hand for only a few mortises. If I had a run of them, I used my Powermatic 701 mortiser (modified with a cross slide vise).
But I found a great deal on an unused Leigh FMT Pro on CL. Since I got it, I've done about 50 mortises with matching tenons for a couple of sideboards and a hutch. It was so fast, precise and easy, that it'll be hard to go back to my old ways. Even for just a couple of M&Ts, I'll reach for the Leigh FMT.
I do a lot of through tenon joinery, so I plan on getting the square tenon templates for the FMT and square up the mortises with my chisels.