含有=contain, have (most common word, can be used to refer to both non-abstract and abstract words); e.g. 这些材料里面含有不少水分。(The materials contain quite a lot of moisture.) 他的话里似乎含有一种对此不屑一顾的意味。(His words seemed to have a sense of contempt for this.)
包含=contain, embody (rather formal or abstract). e.g.这个词包含着丰富的含义。(This word has wide implications.)
包括=include (common word and implies listing), e.g. 语言学习包括听说读写四项基本功。(Language learning includes the four basic skills of listening, speaking, reading and writing.)
含有 and 包含 are similar, sharing the meaning of "contain", with the difference that the latter is more formal. 包括 is almost the equivalent of "include".