Unlike standard ROMs (which are often .3ds files), a CIA is an installable package. It behaves exactly like a game downloaded officially from the eShop. Once installed to your SD card via a homebrew launcher (like FBI), the game appears natively on your 3DS home menu as a bouncing icon.
When users search for "3DS CIA best," they are usually looking for the most reliable way to play games on modified (Custom Firmware) 3DS systems or emulators like Citra. Here is why CIA is the superior format: