How do I best combine several documents?

Question

I have a collection of articles written in latex, and I would like to "merge" them into a larger thesis document, in which each article will be a chapter. I have been looking at include and input, which are great if you start with the meta-document in mind. However in my articles I have sometimes a bit exotic dependencies, such as dot2texi, and using the naive approach fails rather abysmally with all kinds of broken paths.

So I was wondering, do you recommend any "best practices" for merging non-trivial documents -- which packages to look at, or to avoid at all cost, etc.

Thanks