The basic question that this blog tries to address is: 

How much overhead does booking a railway ticket on IRCTC add as compared to booking it the traditional way?

Basically, the extra charges that come into play when booking a ticket online through IRCTC are:

1) Service charge that is IRCTC specific 

2) Transaction charges depending on your payment gateway (HDFC PG, Axis PG, etc...).

Note: 

For AC and first class tickets, the ticket fare itself includes a service tax that's calculated as 14% of the 30% of actual total ticket fare (base fare + reservation charges + superfast charges). 

In your online booked ticket, this is shown by the line that says "**Inclusive of service tax -- Rs XYZ only". More information on this can be found here: http://timesofindia.indiatimes.com/city/allahabad/Indian-Railways-levy-service-tax-on-AC-1st-class-tickets/articleshow/16635956.cms. This article calculates service tax using the old rates, but it was revised to a consolidated rate of 14% of the value of services since June 1, 2015, so use this rate for calculating the services.

However, this should be not confused as being IRCTC specific, because this service tax is also applied in tickets that are booked the traditional way.

Details

IRCTC Service Charge

For normal sleeper class reservation, IRCTC charges Rs 20 + service tax (as of June 1 2015, this tax is 1.4%, so the service tax comes to 2.8 Rs), for a total of 22.8 Rs/-..This is not per passenger, but per ticket (max 6 passenger on a single ticket).

For all other classes, IRCTC charges Rs 40 + service tax (which comes to about 5.6 Rs), for a total of 45.6 Rs/-..This is not per passenger, but per ticket (max 6 passenger on a single ticket).

Transaction Charges

Look up IRCTC for the exact transaction charge because it varies with the Payment Gateway. For HDFC, it is 1.8 percent if you use credit card and flat Rs. 10 if you use net banking or Debit Card. Additionally, you will have to pay service tax on this amount.

Key Takeaways:

1. For a total ticket amount less than about Rs 550, use credit card because 1.8% transaction charge will come to less than Rs 10. And adding 14% service tax, the total transaction overhead charged by your payment gateway will be less than Rs 11.4.  For anything above 550 Rs, think how much additional you're paying and if it's significant, you are better off using net banking or debit card because they charge a flat rate of Rs 10/- + service tax, so you will incur a overhead of Rs 11.4. regardless of the total ticket cost.
2. If you're booking a single ticket that's easily available, for A/C, you end up paying additional 45.6 + ~11 Rs Transaction charge, making it about Rs 56 extra. For sleeper classes, this comes to about 33 Rs (22.8 + 11). For multiple people, the overhead per person become low, so shelling out this extra buck may be okay, but for a single person, this overhead of Rs 56 may be a significant percentage of the actual ticket cost. So, if you have extra time or don't mind sending a peon for buying your ticket, taking the traditional route of going to a ticket window will save you some bucks.