Well, I simply have VirtualBox installed with a Windows XP x32 virtual machine.
Setting it up takes about 20 minutes. Much less than setting up this windows->linux->windows beast.
And it's much more stable than any WINE for windows solution.
Works a treat for all x16 software and the only overhead you got is 4GB of disk space and 500MB of RAM as well as 5% kernel time.
(also, virtualBox is able to pass through 3D rendering instructions on a windows only environment.)
It boots in 15 seconds.
To compare this:
FreespaceSCP gulps up 30GB on my drive and whenever I open my browser it already uses more than 1GB of RAM.
The overhead is tiny for our modern 4GHZ CPUs. The OS does not mind, your system does not mind and the 16bit application certainly gets enough power.
Just use it for all your 16 bit needs and it'll soon pay off.