I believe I've found the most compact design for a timer to control your Mk3+ nuclear reactors. It's fully configurable, you just need to set how long the reactor will stay turned off and how long it will stay off.
If you are not bothered to test to find after how long your reactor will crash and burn, I recommend using this reactor planner, it tells you the cooldown and meltdown times.
Thought I might share as I thought this could help those of you who are kind of new to redstone/RedPower as I know that my very first reactor timer took a lot more space than this, and therefore following this design will keep your timing system compact and easy to hide. Due to this being made entirely with RedPower systems, you could easily fit this on a the outside wall of your Reactor's room, making it even easier to hide.
As an example, here is my nuclear timer set up on the outside wall of my reactor room:
(This design also includes an instant kill-switch using wireless redstone shown in the top right. Any signal sent from that wireless receiver will override the current setting on the timer and turn off the reactor.)