Interesting Thread here. Been working in Tokyo for a few years and basically there are a lot of Malaysian here as well. Most can actually speak good Japanese as they graduated from a Japanese universities. I have a few non Malaysian friends who cannot speak Japanese working here as well. But they were send here initially from their home countries.

Comparing to Malaysia, pay here is good, but the taxes are really high. You need to pay two taxes - municipal and government. Besides that you need to pay to the pension scheme that you most probably wont get back unless you work 25years. Most you can get back is two months worth of salary. On the plus side, since you pay taxes you are treated like a normal Japanese. If you plan to give birth in Japan you get lots of benefits compare to Malaysia.

As for housing, be prepare to live in a small house. If you are single I guess its fine, but with family, you need to get use to it. As mention by @flanegan, you need to pay deposit and Key money as well. However now quite a number of places do not need to pay these. During my negotiation, I negotiated a longer period than the normal 3 years, to get the rent down and no key money. My agent is very good and can speak perfect English. He help me with all the negotiation with the landlord. For two months, every weekend, he drove me around Tokyo to look at apartments/houses until I make a decision. It was really interesting as you get to see lots of Japanese houses design.

Finally you need to be prepare for earthquake. It happens often in Tokyo that it just dont get reported as its not big - average magnitude of 3. But its still unnerving when you feel the building shake.

You can try Rakuten. I know they hired a lot of non Japanese speaking people in their IT department. Google Rakuten jobs and should lead you to their homepage.