We spent 3 weeks travelling round Malaysia.
Set off from the UK with pre-booked return flights to Kuala Lumpur and a hotel for when we got there and also accommodation in Pangkor Laut Resort on Pangkor Laut Island. The rest we booked whilst we were there as and when we needed and wanted to move on from where we were. We used the Lonely Planet and the Rough Guide and basically just went wherever we fancied. We used public transport, long distance coaches, long distance taxi's, internal flights and boats to travel around the different places. We saw some amazing things and had a fantastic experience.
Heres a basic outline of our itinerary:-
We spent 2 nights Kuala Lumpur and then booked 3 Nights in the Taman Negara jungle staying in wooden huts in the oldest rainforest in the world. We then travelled south east to a remote island in the south China sea called Tioman Island, it was truly idyllic with gorgeous beaches and lots of reefs to explore whether diving or snorkelling and also very small with no roads on the island only footpaths. From there we went to Penang Island which was a bit too commercial for us and it was too busy, too many tourists. Finally we stayed in Pangkor Laut Resort which was pure 6* indulgence where we stayed in a sea villa perched on stilts in the ocean. Our every need was well and truly catered for it was an amazingly romantic resort the perfect end to a perfect honeymoon.
I booked my flights direct with Emirates and the hotel in Kualar Lumpur was through e-bookers, I booked Pangkor Laut with Trailfinders. I would highly recommend Trailfinders they are an excellent travel agent, very knowledgeable and have lots of expertise in honeymoons/extravagent holidays. Try and visit one of their shops and just sit with them for an hour or so tosee what they come up with.
Dont forget to consider the weather like for example try and avoid the Caribbean during hurricane season (June - end Oct) etc.
Heres a few links for some of the things I have mentioned.
http://www.pangkorlautresort.com/
http://uk.youtube.com/watch?v=bz_qudd4y_8
http://www.tioman.com.my/
http://www.malaysiaforestresorts.com/
http://www.tamannegararesort.com/packages/index.asp?gclid=CNb--eec-pQCFQ4YQgodBmtfqQ
http://www.tourismpenang.gov.my/
This ruly was an unforgettable holiday for us and we loved all the places we went to the highlight for both me and my hubby was definitely the rainforest, we saw some amazing scenery, exerienced how the locals live, saw lots of wildlike and insects and the rainforest itself was breathtakingly beautiful and glorious. Attenborough and the BBC do a bloody good job of trying to educate us in wildlife and show us how the forests grow and live but its nothing like experiencing it for real, being able to smell, feel, see and hear all the different animals, plants and insects.