Excellent small keyboard by PFU America, Inc. with sensible placement of the CTRL key. New users will find the fn-escaped arrow keys most disconcerting to get used to (it takes a week). The HHKB has "diamond keys", which xev reports being associated with keycodes 129 and 131. You can map the diamond keys to be "Hyper" modifiers under X with something like

xmodmap << EOF
keycode 131 = Hyper_L
keycode 129 = Hyper_R
add mod4 = Hyper_R
add mod4 = Hyper_L
EOF

If this works for you then you can think about putting something similar in your .xsession file.