In IPv4, if I want to send a magic packet to a workstation in another VLAN, I enable directed broadcasts in the remote VLAN and send it to the VLAN's broadcast address. This works great.
In IPv6, I can use FF02::1 to send a WoL frame to workstations inside the same VLAN, but without broadcasts, how would I send it to a workstation in a different VLAN?
On any router or firewall where you can put in static ARP or ND entries you might try to bind an address to MAC ff:ff:ff:ff:ff:ff and then send the Wake-on-LAN packet to that address. If the router/firewall sends the packet onto the ethernet segment with destination ff:ff:ff:ff:ff:ff then you'll have a broadcast packet...
There are no subnet directed broadcasts in IPv6 because there are no broadcasts in IPv6 at all.
One option is to send the packet directly to the IPv6 address of the host (which you of course will have to know in advance, just like the MAC address) and hope that the switch still remembers which port the host is connected to. This seems quite iffy to me and is probably not going to be reliable in all environments.
Long-term the workstations should probably be waking themselves up on a schedule, or not sleeping at all.
WOL has nothing to do with any IP version. The magic packet is send to an Ethernet broadcast address which is the same for IPv4, IPv6 and other protocols.