What connector for Atari 2600 Controller?

The pin-compatible connector that matches the Atari 2600 PCB is TE Connectivity's AMPLIMITE : 5745001-3 PCB D-Sub Connectors.

I know it uses a D-Sub9 connector,

DE-9 to be exact.

• D for D-Subminiature
• E for the shell size of ~19.5 by ~11 mm
• 9 for 9 pins arranged in two rows as 5+4

but is there anything special about it?

No. Despite being of plastic on the controller they are as standard compatible as it gets.

What I mean is can I go on Digikey and just buy any male D-Sub9 connector and it will be compatible with the Atari 2600 controller?

Yes. At least for the plug side it doesn't matter if it comes with or without nuts for fixing it, as they end below the shell line, so the area a plug may need is free. Personally I always prefer ones with nuts, as they offer an option to fix the controller if possible.

While selection of the plug side is painless, you need to select the right connection side for your project straight or 90 degree thru hole or the same for SMD. Some may have additional pins for better fixation on the PCB, so additional holes/soldering areas are needed.

Don't forget to ground the shell - just in case.

It is a standard DE-9 connector, with the exception that there is a plastic shell instead of a metal shell.

Atari Controllers don't have screws, so if you can, chose a male connector without screws to match.