Peninsular Malaysia has a relatively efficient transport system by Southeast Asian standards, and while Malaysian Borneo isn't quite as comprehensive, it's still pretty reasonable. You'll find prices generally higher on Malaysian Borneo. The longest highway is Peninsular Malaysia's North-South Expressway, which stretches for more than 800 kilometres between Singapore and the border with Thailand to the north. Driving is on the left.
Malaysia has two key domestic carriers: Malaysia Airlines (lost two Boeing 777 aircraft within 131 days, with a total of 537 passengers and crew killed; subsidiaries MASWings and Firefly) and AirAsia (its Indonesian subsidiary crashed in 2014, killing all 162 on board). Berjaya Air also has domestic flights.
The main international gateway on Peninsular Malaysia is Kuala Lumpur, which has two terminals (KLIA and KLIA2). Penang and Langkawi both have moderately busy domestic and international airports. In Sarawak, the two main hubs are Kuching and Miri, while in Sabah, it is Kota Kinabalu.
If you book early enough or manage to catch AirAsia on a promotion, the price of a plane ticket can be less than that of a bus ticket. The same goes for Malaysia Airlines or MasWings. A handy hint is that MasWings flights are cheaper than Malaysia Airlines, even on the same routes, as MasWings’ routes are subsidised by the government. You’ll need to book with MasWings if you want to head into the interior or any rural areas – they are often the only airline that operate these routes.
Travelling by the state-run train system in Malaysia is an excellent option for getting around. You can easily catch the train from Singapore to Kuala Lumpur, while another popular route is Kuala Lumpur to Butterworth (the station for the ferry to Penang). From here you can also head on up to Bangkok. Fares are reasonable, the scenery is lovely and comfort (and safety) levels are much higher than on a bus. For comprehensive information on catching the train in Malaysia, you can't beat The Man in Seat 61. Or head straight to Keretapi Tanah Melayu Berhad to buy tickets online.
Getting around by bus in Malaysia can be efficient, though not always safe -- good roads and reckless drivers combine dangerously. Most towns have a bus terminal and tickets can be booked in advance online -- a good idea over busier weekends and on major holidays. Konsortium Transnasional Berhad is Malaysia's largest bus operator -- they own brands including Transnasional, Nice, Plusliner and Cityliner. As across most of Southeast Asia, the air-con can be absolutely freezing, so despite the tropical heat outside, you'll need to rug up to stay comfortable on long journeys.
For more out of the way destinations, you may need to rely on older fan-cooled buses.
On Sabah and Sarawak, buses will generally not have toilets but stops are made every three hours or so for passengers to take a break. You can take a bus, for instance, from Miri to both Kota Kinabalu and Kuching; each trip takes 10-16 hours depending on traffic and road conditions. If you take the Miri-KK bus, you’ll get a stack of stamps in your passport as you cross state and country borders more than once.
These can be found in most towns. Drivers wait until they have four passengers before departing for their destination, or you can hire the whole car yourself (paying for four seats). Prices should be set and posted at stands.
Roads are usually decent, it's easy to hire a car from operators such as Avis and Hertz, and fuel is relatively cheap. Malaysian driving can often be quite erratic and takes some getting used to, particularly within cities. Pedestrians should also take care as drivers often do not appear to take them into consideration. Speeding on highways is a dangerous problem too.
Hitchhiking is quite common among locals in Malaysia, although some drivers may charge so clarify this before getting in the car. The normal rules apply; it’s always safer to travel in a group, you won’t get picked up at night and be mindful that most locals have lax rules when it comes to drink driving.
You'd be forgiven for thinking you could, but sadly you can't catch a boat between Peninsular Malaysia and Malaysian Borneo. Plenty of boats run between Malaysia's mainlands and closer offshore islands though. While better than neighbouring Indonesia, ferry standards are often sub-par; if you think a boat is not safe to board, trust your judgement and skip it.
Malaysia boasts decent roads for cycling, with mechanics usually easy to find. You can often rent bikes from guesthouses for a daily rate -- make sure they come with a chain to lock up when you park.