The Johor Bahru Customs, Immigration, and Quarantine Complex (CIQ) is a very large complex at the causeway to Singapore that accommodates Malaysian customs check for cars, trucks, buses and the JB Sentral train station. The CIQ was opened in 2008. The complex is know as CIQ – if you tell a taxi for example they will know where you mean to go if you say CIQ.
Queues are often reasonable but at rush hour (especially leaving Singapore on Friday’s and near public holidays) can be long. In several ways taking the bus is quite appealing (costs of bringing a car into Singapore plus tolls and there are significant restrictions on taxis that make that option difficult) but the walking from the entrance to the custom lines is quite a distance so that will add 5 minutes to your time. And waiting for a bus once you clear customs can add another 5 – 10 minutes. [update – given all the long delays and complaints from people they reopened walking over the causway as an option. A newspaper story in 2016 claimed 300,000 people walk across each day, that surprises me and I am not 100% sure the number is accurate]
The 2nd link (to the West) has shorter queues currently (these are the only 2 links between Singapore and Johor Bahru now). That is one of the reasons many people have been buying out near the 2nd link. Also that is a focus area for the Iskandar economic development initiative and the available of housing estates with integrated security and new bungalows is another attraction.
JB Sentral, which opened in 2010, is located in the same area and includes the train station and a large bus terminal.
Singapore and Malaysia have been taking recently about extending the MRT (light rail) from Singapore into Johor Bahru before the end of this decade and the likely location of the first stop is JB Sentral. This MRT (and extending 5 to 7 more stops in Johor Bahru will be a welcome improvement to mass transit and continue to build the economic ties between the two cities. Currently you have to take the long walk through Malaysian customs, then walk to the bus, take it over the causeway, walk through Singapore customs, catch the bus again and then got to the MRT (which for some reason isn’t the closer Woodlands MRT but the Kranji MRT). So just getting on the MRT in JB and clearing customs and getting right back on will be a big improvement. Of course they will have to add quite a few more customs staff to prevent long queues.