Which "silkscreen" process for home-made PCB prototypes?
Toner tranfer is probably your best bet.  Look up how people make PCBs using toner transfer.  Make your pcb by any method you like, then after it is etched and clean, use the toner transfer method to put the part markings on the board.  Of course, you leave off the etching after this second toner transfer.

The markings won't hold up like real silk screen, but its really about the only solution available.