>> Besides considering the price for traveling, are there any entrance fee required for Mt Rigi, Mt Titlis and Jungfraujoch?
No, there are no additional entrance fees for visiting the mountain tops just for sightseeing, but if you also want to do some of the activities, they do cost extra e.g. Ice Flyer, tobogganing, scooter bike etc at Titlis; Snow Fun Park at the Jungfraujoch.
>> Also, I visited the Mt Titlis website and the price table kinda confuses me. It says Engelberg to Titlis cost 92CHF for round trip?
Yes, that is the full fare. With a Swiss Travel Pass you will get a 50% discount on that fare.
>> What are the other pricing that says from Engelberg to Stand, Engelberg to Trubsee etc? Are they stations along the way?
Yes, those are intermediate stations on the way to the top of Titlis. You can read more about the route here:
The price structure caters for people who only want to go part way, as well as for those who want to go right to the top.
>> If we want to explore instead of going straight up to Titlis, we have to pay more?
No. Your return ticket Engelberg-Titlis is valid all day, and allows you to get off at either or both of the intermediate stations. If you plan to do this, I would do it on the way down rather than the way up, in case the clouds roll in and block the views from the top before you get there.