I have found that flying into/out of Malaysia is much cheaper than the same through Singapore. On my way to Siem Reap I had to fly out of the airport at Johor Bahru, but I was stationed in Singapore!
After some digging I found the taxi stand at Rochor Rd. If you can get to Rochor Rd., it seems there are taxis there 24/7 waiting to take you to Johor. I think the standard charge to the JB airport is like SGD $60.
The Malaysian taxis can take you the whole way, the Singaporean taxis cannot. And especially if your flight is early, it is hard to get to Rochor Rd. because you have to pay a taxi and all its booking fee & midnight surcharges to get you there.
The solution for me I found at Rochor Rd., a Singaporean taxi that can pick you up from your residence for an additional fee and then transport you into Johor. The Singaporean driver arranges a reliable Malaysian driver. You pay the Singaporean driver, and he will pay the Malaysian driver so there is no issue of haggling in Malaysia. The whole process was very smooth for me at cost me SGD $70 for a pick up from home and direct delivery to the Johor Bahru (Senai) airport.
I wanted to share some numbers for those who find themselves in the same predicament. It will save you a trip to Rochor Road to figure it out.
For a Singaporean taxi that can pick you up in Singapore and make the connection to a second taxi in Malaysia. I dealt with both gentlemen and they were quite professional.
Henry +65 9107 7728
Alfred +65 8233 5155
For a Malaysian taxi that can pick you up at Rochor Rd. and deliver you:
Din +606 012 7895854 or +606 02 91604149.
I haven't dialed Din's number myself as I met him in person and he called me - so you may have to take out the zero after the country code, for example: +606 2 91604149.
Hope this is helpful!