There are multiple types of RGB LED headers. The most common is the typical RGB LED header with a 12v pin and R, G, and B pins. RGB LED strips group all LEDs together, so you cannot individually control each RGB LED. Digital/Addressable RGB headers connect to digital RGB strips; they allow you to individually control each RGB LED in regards to brightness and color.
Digital/addressable RGB control is not that amazing right now, and there are many types of headers for digital/addressable RGB LEDs. There are also RGBW LED headers, that provide one extra rail for RWGB strips that provide one white LED for each RGB LED to provide true white. One vendor has gone and added a jumper to control whether the digital strip uses 12v or 5v as its power source.
One vendor calls their addressable/digital RGB header a JRAINBOW header, it strictly uses 5v, and looks similar to another vendor's AURA addressable RGB LED system. The vendor that has a JRAINBOW header also has a JCORSAIR header, which is basically a digital RGB header with a different pin-out made for Corsair RGB accessories.
Basic RGB LED control or digital/addressable control has to be done by a microcontroller, on one brand the chip is labeled AURA. On another brand, they use an ITE8295, which is basically a microcontroller. If you find a lot of these chips on a motherboard, chances are the motherboard provides a lot of addressable/digital RGB LED control. These controllers are typically microcontrollers, and you typically can't find much information on them.
While most fan headers look the same, they can greatly differ depending on how the vendor has implemented hardware. These days, most headers on a motherboard can be configured in PWM or DC mode, sometimes they limit the CPU fan header to only work in PWM mode.
On the two motherboards above, I have circled headers in yellow (on the left) and blue (on the right) that provide more amps (2-3 depending on board). Most fan headers provide 1-1.5A depending on brand and motherboard, so supplying more allows for daisy chaining or powering high amperage pumps. On both of the motherboards above, I have circled (in green) external temperature sensor input headers. You can use those headers to control headers, so you can place a sensor in your GPU's heat sink and have a real GPU temperature to work with. Motherboard manuals, and honestly, marketing materials, will tell you about fan features.
One vendor has watercooling specific temperature and water flow headers. We also find Water Pump headers that typically run full speed by default. One vendor actually has full-speed headers that operate at full speed all the time and cannot be controlled.
Typically, the SuperIO controller (on the left) handles most of the fan control, but these days we find a lot of secondary embedded controllers (on the right) that expand fan control and temperature monitoring.
We might also find individual fan header controllers near each header that provide extra features and power. Some vendors implement many smaller controllers to monitor temperatures and provide extra control.
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