1.We think that that is which appears to be.
句子来源：http://www.youdao.com/example/which%20appears%20to%20be/#keyfrom=dict2.TOP
这句话中的从句which 已经做主语了，后面的be缺少宾语，如何理解？
我的想法：which appears to be整体作为一个 it 。
还是这句话本身就不对？
2.If I said,Whatdoyouthinkmost Christian religious people believe aboutwhathappens toyouafteryoure dead?
句子来源：http://www.youdao.com/example/mdia/video/what_do_you_think/#keyfrom=dict.main.sentence.mdia.video
意思我懂。但此句中 do you think 后面的从句中不缺任何成分，那样what 代指什么?作为think的宾语吗？不太理解。
好比这句（自己造的）：what do you think he is a nice man. （不了解这么写行吗？如若哪儿不对，怎么样改正？用do you think 。）
3.Whatdoyouthinkare those that are likely to come up in this debate?
句子来源：http://www.npr.org/templates/story/story.php?storyId=4655615
此句去掉 “do you think”完全了解，有人说这是插入语，就如此。感觉心里不是滋味，不是非常理解，怎么样细致地剖析？
我的理解：what做 do you think 宾语的同时，还做“are those ... ”的疑问代词。
望各位老师不吝赐教，感激不尽。
1. We think that that is which appears to be.
本句正如网友所言：be之后缺少表语，假如添上一个比较级形容词就能了，比如：better。
如此，which appears to be better 是表语从句，第一个that 引导宾语从句，第二个that是指示代词，比如，指代疑问定义的the question, the problem 等。
我把句子补充完整后，是这个样子：
We think that the question is which appears to be better.
【翻译】大家觉得，问题是哪一种（方法）更好。
2. If I said,What do you think most Christian religious people believe about what happens to you after youre dead?
【翻译】假如我说，“你觉得大部分基督教教徒对你死后发生的事有哪些怎么看？”
本句是一个条件句，缺少主句。
就这个条件句而言，没错误。
do you think 是插入语，去掉后：
What do most Christian religious people believe about what happens to you after youre dead?
本句中，What 是believe的宾语，about后面的成分是一个名词性从句含有空闲状语从句。about表示“关于；对于”。
What do you believe about...? 句型：你对......有什么怎么看？
3. What do you think are those that are likely to come up in this debate?
【翻译】你觉得在这次辩论中可能出现的问题是什么？
do you think 是插入语，去掉后：
What are those that are likely to come up in this debate?
that are likely to come up in this debate 是those 的定语从句。依据定语从句中come up 的意思，those 非常可能指代“问题”，然后用that 引导定语从句修饰它。