I like to do pyramid sets with pullups, dips, and pushups. Start with 1 pullup, 2 dips, and 3 pushups then 2 pullups, 4 dips, and 6 pushups. Continue that 1x, 2x, 3x structure until you can't do anymore than go back down the pyramid to 1,2,3. Try to do it with as little rest as possible to keep your heart rate elevated.
Also if you struggle with pullups, I always reccommend the Armstrong Pullup Program, http://armstrongpullupprogram.com/
. It's a great way to quickly boost how many pullups you can do which is important because pullups are by far the most important bodyweight exercise.