a thread from JWFan.com about this very topic--a couple of the people there also mentioned that the 1997 and 2004 discs are identical in sound quality, but the 1997 discs have better liner notes (I agree that the 1997 liner notes are excellent--haven't seen the 2004 liner notes myself), and that the only real reason one would get the 2004 discs is because of the exclusive screensavers--which I read somewhere weren't all that great, anyway.
I'd say go for the 1997 sets, if you can find them, for the better packaging and liner notes.2004 box set for $50 at DeepDiscountCD
The individual 2004 discs look like they go for around $20 each at Amazon and DDCD, so $50 for the box isn't that bad a deal.
Looks like the 1997 discs are OOP and OOS at those stores. I'd say eBay may be your best bet for the 1997 versions. Here's
one for all three sets with the hard-to-find exclusive slipcase for $35 plus $10 for shipping.
And there's a couple of auctions for the 1993 Trilogy Anthology box up on eBay, too. Like I mentioned, there's not as much music on that set (four discs as opposed to six, if you combine the later sets), but there are the exclusive lost tracks, and a couple of other weird mix-and-match tracks in that set, too. And that's got some nice packaging, too--including a pretty nice booklet with some different liner notes and some fairly rare photographs and artwork. Plus, those sets are only around ten bucks or so on eBay. So that set may be worth tracking down as well.
Of course, you could always wait and see if they do anything new for the 30th anniversary next year, as some of the guys at the JW site seem to think they will. . .