I've used VoodooPad for a while as a generic translation tool. You could select text, and make hyperlinks to other documents inside the VoodooPad project. So each time the same term is shown in the Wylie document, the underlines show up and I could follow and see what term I used before.
VoodooPad 3.2 is even better! Note the image, now if I command-control and hover the mouse over the link, the first lines of the linked document shows up. So I could just scan over the document and quickly see a rough translation based on earlier terms.
You could build up your own Dharma-vocabulary system this way, and be very consistent how you use terms. Also, you could take entries from dharmadictionary and other sources, and just add these into the same project, and you could slowly build up your own customized translation system. Pretty neat, or what!
I don't know if there's a corresponding Windows application that does something similar -- this is MacOSX only. Also, there's a free version and a very cheap full version, as well, so you could first try out the free one.