There is a note attached:
I've seen you change and grow. A bit like me, actually. So here's a gift for the two incarnations of Nathan Petrelli. Happy Birthday. -the Doctor
Chivas Regal Royal Salute, 50 Year Old, with a note attached: For you as I first met you.
Lutherian bible, circa 1545, with note attached: For you as you are now.
The Doctor may not understand Nathan very well (alcohol and Earth religion?), but that doesn't mean he won't try to respect him.