We are a group of 4 travellers from India, travelling to bangkok from 24th December to 5th January 2013.
During these 12 days I wish to visit Kualalumpur, pattaya also. Want to spend new year eve in Koh Samui. I would like to use all cheaper means of transport so as to save cost of travel. Please help me in making itinerary.

You will be travelling at the most expensive time possible for hotels and transportation. I would start checking on hotel prices and availability right now and for Thailand try using: http://www.sawasdee.com

As for the least expensive means of transportation in Thailand try bus and/or train. You will waste more time travelling like it will take you the whole day to go by bus or train to Koh Samui and then you will need to take the ferry to the island proper as well. The savings will be significant though.

Again start reserving the hotels in Bangkok and Samui and for X-Mas and New Year make sure the hotels does not require for you and your group to attend a mandatory paid(extra) dinners or events.

I'd advise you to re-think your plan. In 12 days, you plan to go to 4 destinations, and you plan to travel overland, so some of these will take a full day, leaving you an average of two full days at each place. I'd suggest you start by cutting Pattaya. You are going to a nice beach in Koh Samui, why go to a not-very-nice beach at Pattaya?

Also, is KL a must-see for you? I find it a much less interesting city than Bangkok. If you do go to KL, plan to fly Air Asia rather than taking the train, which is a full-day trip.

<<why go to a not-very-nice beach at Pattaya?>>

Most likely not the OP's intention, but I can think of a few reasons why people go to Pattaya--none of them having anything to do with being near a beach unfortunately.

Kathie, we have changed our plan and dropped KL. Will stay only in Thailand. Bangkok, Pattaya and Koh Samui. Tentative plan is 24-25 in Bankgkok, then to Pattaya and back to Bangkok for train travel to Surat Thani and then travel to Koh Samui for New year's eve. On 3rd Jan, back to Bangkok for return flight on 5th Jan. to India.
Any other suggestion to change logistics? Is any ferry travel will save time?
Filmwill, you are right, being on the beach is not a priority, but certainly want to watch and enjoy.