Back when I made my own boards, I used a modified pad shape (okay, I wrote my own layout program) with a tiny little hole in the middle, and after developing the board, the hole provided just enough of a dimple to guide the drill.

I made my last homemade board, some kind of electronic music circuit, in 1993. Today, there are so many interesting chips that are sold as breakout boards by Adafruit, Sparkfun, and the like, that it's easy to prototype by just stringing wires between boards. For the next level -- has to be nice but not commercial and not on my own nickel -- ExpressPCB is my friend.