You can obtain HexClock.exe immediately after completing Bit's second mission, "Getting some tools together". Just get your copy of SSHcrack.exe and you have all the necessary.

1) Connect to Viper-Battlestation (the IP is given to you Bit in his second email)
2) Use the "scan" command to find the Entropy Asset Cache machine and connect to it
3) Solve the firewall (password: time), and hack one of the four possible ports
4) Once inside, the file will be in the /bin folder. Just scp it to your workstation and you're done!

(Thanks to Ass_Blastem69 for the corrections)

An HexClock is a clock that converts time (format: #HHMMSS) into an hex value, and changes its background color accordingly.
In Hacknet's case, the change of color affects the whole UI's palette, and the effect is something like this: