When you write a paper, your ideas need to flow smoothly. If the reader must struggle simply to keep up with your train of thought, then you have written a poorly designed paper.
One way in which to ensure your ideas fit together neatly is to use transitions. Transitions are key words or phrases which assist you in joining your thoughts and ideas. They can be used to link paragraphs together, or they can be used to link sentences in the same paragraph.
Transitions can be grouped in catagories, according to their specific uses.
To show how similar ideas are:
To show how ideas contrast with one another:
on the other hand, but, yet, nevertheless, still, however, otherwise, on the contrary
To add more ideas or thoughts, or to group a series together:
first, secondly, also, finally, as well, in addition, moreover, in conclusion, furthermore, in the first place
To show emphasis, or to clarify thoughts:
after all, indeed, nonetheless, in fact, for example, to illustrate, in other words, as a matter of fact
To indicate a result:
for this reason, because, hence, accordingly, as a result, since, therefore, since, consequently
To indicate time:
then, afterwards, after, next, until, consequently, once, meanwhile, later
These groups are not meant to be a complete list. There are many more transitions which may be used, and a single transition may fit into more than one category. What is important is that you realize transitions are necessary for smooth, clear writing.