here ya go http://mlb.mlb.com/mlb/standings/mlb_standings_2001_season.jsp
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The St. Louis Cardinals had the best regular season record in 2005, going 100-62. http://mlb.mlb.com/mlb/standings/index.jsp?ymd=20051002 (full standings for 2005)
Final Standings
Yes. All regular season games count towards standings, no matter who the opponent is.
The 2001 New York Yankees
The most wins in a season before the schedule was increased to 162 games was by the 1906 Chicago Cubs who won 116 games. This is still the record for most wins in an MLB regular season. It was tied in 2001 by the Seattle Mariners.