When Windows loads it's Startup file, it attempts to load every program in there at the same time. Therefore if you have quite a lot of programs starting when Windows starts, each program will try and grab CPU and Disk time so that it can load.
If each program tries to do this at the same time, you soon notice the slow down that occurs due to your CPU trying to help all the programs to load, and your hard disk accessing multiple files.
Startup Delayer allows you add some order to this process by determining the best time to launch your Applications. You can choose to do this based on how idle your computer is, or you can set an arbitrary time.