There were changes made between 1998, 2001, and 2002, again in 2004, 2005, and 2007. The most significant being the 2004 and 2007 changes.
Steve or Mark at GoFasters can probably fill you in on the specifics of each change.
In 1998-2002 there were XC200's and EC200's. The XC being the stripped down full race version with smaller coil and no lighting and the EC being the full enduro version with larger coil and enduro lighting. In 2003 the XC became the DE and the EC remained the same.
I have an '03 EC200 and love it. There is nothing wrong with any of the model years though. The 04 frame is probably one of the best turning. There were few changes to the motors on the 200's.
Suspension can be different depending on what month the bike came off the assembly line. I have the full Ohlins. The pre '04 WP/Ohlins is good, but my experience is the WP's were droolers. The seals were constantly leaking. The post '04 Marzocchi/Ohlins is awesome. I haven't had any experience with the Zoke/Sachs set up, but I've heard it is on par with the full Ohlins.
You can't go wrong with any of the years as long they weren't raped by the previous owner. If it's a good deal, and you are happy with the condition of the bike, go for it. Check the subframe for cracks on pre-07 models before buying.
If I were you, looking for a used bike - I'd look for an '04 or '05 DE200. If you can afford new, I'd wait for the '08's to hit the shores. There will be a significant difference in price between used and new. Used Gassers aren't known for thier investment potential. Buying a brand-new Gasser is a purchase based only in hot-blooded passion, not sound economic logic.