For games use a loader (Steam, Origin, etc).
For system software (CCleaner, defrag etc) put everything in the Start button.
For essential software that you don't want it to use with "Start with Windows" put into the task bar.
Delete every program shortcut that can fit in the notification area (like the Antivirus).
Hide every icon in the notification area that you don't need when inactive (like the Action center).
Delete every program shortcut you don't need (WinRar).
Put everything on your User folder. If you have A LOT of stuff, make multiple folders on your desktop for easier access.
Mine looks something like this:
The three folders above are personal files and projects (blue), work (green), games (should be white but I cba). I use GIMP frequently so I keep it on the desktop. Same goes for MTG: O. Breath of Death VII is the game I am currently playing. If I press the Start button, I can access to all the programs to improve my PC (CCleaner, Disk Defrag, etc). On the taskbar, I have the web browser, mIRC and a music player. On the notification area I have mIRC (I like how it bleeps when there is activity), Skype (to change the status fast), Steam (I don't like keeping it open, so it's there), Ad Muncher (I can check when it's active by seeing when the cow goes omnomnom), Wifi and audio (to check the strenght/power). I am considering to remove the clock because I have it on my keyboard.
Mine is just an example, but you can definitely organize without any software.