It depends how much time you have, really. You could just hit the main spots below, or take a couple side trips in Malaysia (ex. Perhentian Islands, Cameron Highlands).
The basic overland route is:
Bangkok -> Southern Thai islands (your choice) --> Had Yai (town on the border wih Malaysia) --> Penang --> Kuala Lumpur --> Singapore
You can also fly cheaply to Singapore from Phuket, Kuala Lumpur and (soon) Penang (www.airasia.com www.tigerairways.com).