Controllers
For information on stock/OEM controllers, see the /components/controllers.md page under Components.
There are a handful of aftermarket controllers that allow a more extensive range of modification possibilities.
Hasu/TMK
The first aftermarket controller available for purchase. This series of controllers was designed by hasu and is supported by multiple firmwares including TMK and QMK.
There are a range of controllers for various HHKB models, including the Professional, Professional 2 (ANSI and JIS) as well as Bluetooth controllers for the Professional 2 ANSI and JIS models.
These controllers do not work with the HHKB Professional Classic or Hybrid series.
The Professional 2-compatible versions of this controller do not include USB ports (as on the factory controller). In place of USB ports, there are two LED indicators and a power switch that fit into the USB port cutouts on the Professional 2 case.
See this thread on Geekhack for detailed information and ordering instructions. I'm not aware of whether hasu sells these controllers via other venues.
Yang
Reddit user /u/yangdigi created a series of controllers with Bluetooth support called the BLE.
A version for the Professional 2 line was released by KBDFans. /u/yangdigi also appears to have created a version of the controller for the Professional 1 line. This controller is no longer available for sale, and unfortunately KBDFans has taken the product page down, so there's not much more information I can provide.
This controller includes a few interesting features, including LED indicators that shine through the HHKB top case (potentially ineffective on charcoal cases), external USB ports (not present on the Hasu controller) and an additional internal USB port which can be used for USB drives or other small USB devices.
According to users, this module provided better battery life than the Hasu controller as of 2020.
This controller doesn't appear to support TMK or QMK firmware. The official firmware appears to be a fork of TMK.
Cipulot
Cipulot created a line of replacement PCBs and daughterboards for the HHKB Professional 2, HHKB Professional Classic and HHKB Professional Hybrid lines.
While it looks like these controllers require both daughterboard and PCB to be replaced, they offer a lot of compelling features. The EC Pro-2 Hub DB replaces the mini-USB plug with USB-C, has two USB 2.0 ports and an additional internal USB 2.0 port for use with accessories like dongles (eg, your wireless mouse's RF dongle).
More information and purchase links available from CannonKeys.