Paragraphing is an important tool in transcripts and should be used frequently, in my opinion. Paragraphing frequently helps the reader easily parse out separate and distinct thoughts and keep track of what he's reading better. In my opinion, a new paragraph should be inserted:
1. To separate the actual question from the preamble.
2. After three to five lines, is possible. Of course, this depends on the paragraph and if it's able to be separated.
3. Every time a speaker says a quote from a new person. "He said..then she said..."
These are all just my personal opinions, of course. Take 'em or leave 'em. Here's a good guideline from this site - http://owl.english.purdue.edu/owl/resource/606/01/
How do I know when to start a new paragraph?
You should start a new paragraph when:
* When you begin a new idea or point. New ideas should always start in new paragraphs. If you have an extended idea that spans multiple paragraphs, each new point within that idea should have its own paragraph.
* To contrast information or ideas. Separate paragraphs can serve to contrast sides in a debate, different points in an argument, or any other difference.
* When your readers need a pause. Breaks in paragraphs function as a short "break" for your readers—adding these in will help your writing more readable. You would create a break if the paragraph becomes too long or the material is complex.
* When you are ending your introduction or starting your conclusion. Your introductory and concluding material should always be in a new paragraph. Many introductions and conclusions have multiple paragraphs depending on their content, length, and the writer's purpose.