Singapore to Malaysia border checkpoints with customs and immigration checks are at:
1. Changi Airport - airlines flying Singapore to Malaysia.
2. Selatar Airport - scheduled flights from Singapore to Tioman island (Malaysia) and Batam (Indonesia).
3. Road link - Causeway link from Woodlands checkpoint (Singapore) to Johor Bahru city, Johore (Malaysia)
4. Road link - the Second link at Tuas, Singapore - road links to the North-south (PLUS or toll) expressway in Johor, Malaysia.
5. Railways - from Woodlands, Singapore for Singapore immigration and at Tanjong Pagar (Singapore) for Malaysian Immigration. (Confusing?!); from JB railway station, you can travel to KL, until Padang Besar and to Thai railways, up to Bangkok.
6. Ferry treminals and checkpoints - from Singapore to JB: Changi point ferry terminal, Tanah Merah terminal, Changi ferry terminal.
7. Singapore Cruise Centre, Harbour Front Centre, at Maritime Square - for cruise ships going to Port Klang or Langkawi.
Details of transport options and how to get to Malaysia from Singapore at: myMalaysiabooks