Best in terms of current world champion is JUNIOR.
See list below of past champions.
World Computer Chess Championship
Champions of the WCCC
12th WCCC 2004 Ramat-Gan Junior
11th WCCC 2003 Graz Shredder
10th WCCC 2002 Maastricht Junior
9th WCCC 1999 Paderborn Shredder
8th WCCC 1995 Hong Kong Fritz
7th WCCC 1992 Madrid Rebel
6th WCCC 1989 Edmonton Deep Thought
5th WCCC 1986 Cologne Cray Blitz
4th WCCC 1983 New York Cray Blitz
3rd WCCC 1980 Linz Belle
2nd WCCC 1977 Toronto Chess 4.6
1st WCCC 1974 Stockholm Kaissa
The link to the official computer chess association is:
http://www.cs.unimaas.nl/icga/news/WCCC/
In terms of best , i.e user friendly and most popular, Fritz ranks very high , and the program can be found and purchased on
http://www.chessbase.com
The Chessbase company sells a variety of programs including Junior, Shredder, Fritz ,etc.