Most visitors to Malaysia will arrive at Kuala Lumpur's (KL's) international airport, spend a day in the capital, then run around the country trying to see as much as they can in a short span of time. While it's natural to want to maximize your vacation time, I am of the philosophy that to try to pack too much into your holiday will actually detract from your overall travel experience. I've advised countless people on their trips and have been horrified to see some of the itineraries put together by well-meaning but ill-informed travel agents in the West. Many are absolutely exhausting, some physically impossible. I recommend that you see no more than three destinations in 1 week, preferably only two. That way, you have time not just to see the sights, but to stop and feel the rhythm of local life -- to eat the food, smell the smells, speak with the people.
The itineraries I've suggested are all based on 1-week stays in Malaysia. Each itinerary differs depending on your point of interest: Do you like historical sights and museums? Do you want to appreciate nature and explore the great outdoors? Or do you just want to relax on the best beaches, scuba, or snorkel?
A major consideration when planning your trip is the heat. Especially if you're not used to it, the heat and humidity can sap the energy from you. By the time you've finished lunch, you'll barely have the stamina to keep up with the rest of your planned activities. Combined with jet lag, you'll be asleep before dinner. Not a swell time. Keep daily itineraries simple, and make time for afternoon coffee or tea.
Also, when flying between cities domestically, budget your time like this: One flight will take about a half-day. So if you're flying from Penang to KL, set aside either a whole morning or a whole afternoon for the flight. That will include airport transfers and whatnot. Along the same lines, all domestic flights either originate or end up in KL. What this means is, if you're flying from Penang to, say, Kota Kinabalu, you'll fly from Penang to KL in the morning, have lunch in the airport, then spend the afternoon flying from KL to Kota Kinabalu. It could take a whole day.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.