I have two IP addresses bound to eth0, one on device eth0 and one on device
eth0:0.  When I do a traceroute to an address which routes through eth0:0,
traceroute by default uses as its packets' source address the address bound
to eth0, which means that none of the traceroute packets ever make it back
to my machine (since the address on eth0 is a local-network-only address).

Traceroute should be smart enough to determine what interface its packets
will route through and automatically use that interface's address as the
packets' source address.