Many important stations of the Indian Railways have bypasses. These are used to reduce congestion, and especially where a reversal is eliminated.
While some are used mainly by goods trains, there is an increasing trend for more large junctions to be bypassed. In most cases a smaller station nearby is used as the “proxy” for long-distance trains to stop. Examples are Perambur for a few trains which skip MAS, Sevagram for Wardha Jn, Uslapur for Bilaspur, Pathankot Cantt (ex Chakki Bank) for Pathankot.
Here is a pdf file for all of the bypassed stations which I could think of. Additions and corrections are welcome.
Let us not consider “area bypasses” such as Vasai Road-Panvel or Gudur-Renigunta-Katpadi or Kharagpur-Asansol.
Perhaps we can think of a few more places where bypasses would be useful, such as Sawai Madhopur.
Trivia: the first custom-built bypass was probably the one at Shoranur which was commissioned in the early 1940s. Others which came up over the years due to realignments etc would be Allahabad-Chheoki and Podanur, (Yes, I know that the lines around Coimbatore have a complex history).