KOF '98 is and will remain not only the high point of the KOF series, but the best KOF released on the Neo-Geo system by far.

Here's hoping that SNK Playmore finally gives us something that will top it in the form of KOF 2004; I definitely feel that KOF 2003 is a step in the right direction.
Don't see how anyone can choose KOF '99, KOF 2000(as of right now, no one has), or KOF 2001 as the best (strikers = meh, although I certainly have enjoyed those games, just nowhere near enough to be in the top 3), but I guess that's just me. :P
Here's my ranking:
1. KOF '98
2. KOF 2003
3. KOF 2002 (just barely under 2003)
4. KOF 2001
5. KOF 2000
6. KOF '99
7. KOF '97
8. KOF '95
9. KOF '96
10. KOF '94
I know it isn't developed by SNK Playmore, but I'm very interested in seeing where KOF Neo Wave will fit into this list. Likewise with KOF Maximum Impact. I didn't add KOF EX (bleh!) or EX2 (awesome!) to the list because I still consider them ports (of KOF 2000), even though KOF EX2 has several new characters.
Lee