From the KEGG web site:
"The KEGG database will continue to be made freely available on the web.
We are encouraged with the increasing popularity of the KEGG web service
– the number of unique visitors per month has now reached 400 to 500
thousand and has more than doubled over the last three years. With your
support KEGG will be sustainable as a most advanced, high-quality
database meeting the changing needs of biological science." [
1]
So, unless you are going to use the FTP service, it seems as if you can continue to use KEGG web services freely. However, that being said, this is a Cytoscape help-desk and we are not affiliated with KEGG in any way, so I would contact KEGG for a definitive answer.
-- scooter