The way he did it was different ---we were used to.

这个问题真好!
答案是c
注意这里是宾语从句不是定语从句.
The way (he did it) was different from what we were used to.
这里what we were used to 做介词from的宾语.
之所以用what不用which是因为：
what表示一个总体概念,它一般不用在有具体选择范围的句子中.
which则表示在一个具体的范围内进行选择.试比较：
I want to know what book you like to read.（总体概念）
I want to know whick book you like to read best of the three.
（在三本书里面选择）
What food do you like to eat?
Which food do you like to eat,fish or meat?(在两者中选择)
显然原句中的we were used to"我们习惯的（方式）"只是一个总体概念,故用what.