Map your course wisely: Try to avoid sections that a lot of workers commute to.
According to the transport ministry, the 10 most congested lines in the greater Tokyo area were the Tozai subway line, the Odakyu line, the JR Yokosuka line, the JR Chuo line, the Tokyu Denentoshi line ( to Shibuya), the JR Tokaido Line, the JR Sobu Express, the Chiyoda subway line and the JR Keihin Tohoku Line.
Some maps can also be deceiving to the eyes. A ride two subway stops away could actually be a quick walk, well worth the extra time compared to a rush-hour train. (However, keep in mind that the opposite is also true: some JR Yamanote Lines
Stations have almost 2 kilometers between them!)