Automatically-launched programs are often useful applications like virus scanners and firewalls. However, Windows' auto-launch facilities are also used by annoying and even malicious programs and viruses that just waste system resources or actively cause damage.
If you find a dubious entry in the list like HOHOHO.EXE you should deactivate it with StartUp Tuner and then restart Windows® and test all your normal applications.
If everything seems to be working okay and nothing you need is gone (for example icons in the taskbar) then it may have been a malicious program. You can also conserve system resources by deactivating programs you don't need.