Except for the mini-games, the game is entirely controlled with (on Windows) or + (on WiiWare). Simply point and click on objects to interact with them. Clicking anywhere on the ground will make Strong Bad walk there (unless that location is inaccessible). Double clicking on a spot will make Strong Bad run, which is faster than walking. On Windows you can pause the game at any time by pressing . On Windows will interrupt someone speaking, skipping forward in the dialog, or ending it.
Strong Bad's Cool Game uses a very simple interface. Clicking on the bag icon opens your inventory, where items you have collected are automatically stored. The map icon opens The Map, which you can use to instantly travel to various locations in Strong Badia. The camera allows you to take screenshots of the game at any time except for conversations and cutscenes (at which point the interface is hidden from view). On Windows these are stored in a subfolder in your My Documents folder, while on WiiWare they are stored on the Wii's memory. Finally, the gear allows you to access the menu.
To talk to someone, simply click on them. Various icons will appear showing what topics you can ask that character about. Using some conversation topics may open up others, and progressing through the game will add and remove various topics. Some characters have only one or two conversation topics. Choosing the icon showing the head of the person you are talking to (if it is available) will let you compliment or insult a character by choosing the appropriate symbol, which results in a variety of responses.