I have six 7-segment displays, and 3 multiplexing phases. This means that I need to make two groups of three displays with respect to the cathodes, and three groups of two displays with respect to the anodes (because these displays have a common anode). Here you see the result of much tinkering. The outlines of the displays are shown in black felt pen (the markers you use to write on CDs are also ideally suited to draw on circuitboard).
Underneath is one of the displays, for scale.
All the displays in place (though not yet soldered). The wires above and below will be obscured by the face plate of the clock, but I think you would still be able to see the six wires running between the groups of the displays. I'm not sure that would bother me overly much, though.
The driver print for the ICs (apart from the microcontroller). The three 16-pin sockets at the right side are for shift registers: the two right-most are for the 7-segment displays (one 8-bit shift register each), the third is for the LEDs of the binary part of the clock.
The 14-pin socket to the left is for the quad AND-gate IC, which in turn drives the three transistors at the left end of this circuit. These three transistors will be used to multiplex the 7-segment displays.
The shift registers will have to sink the current from the 7-segment displays, which means the leads will have to be protected by resistors. To save space, I mounted the resistors upright.
To close it off, a faux-artsy photo of the row of IC sockets.