The `align` of `alignat` environments (from `amsmath`) seem the way to go here; in some cases you could use `\intertext` (or `\shotintertex` from the `mathtools` package) for interrupting some multiline displays while still maintaining the alignment points.

EDIT: As a side note, the set of equations in Example 2.2 (in the document you linked in a comment) that goes after "*Then,*" was probably typeset using `eqnarray`; you should avoid using this environment since the spacing surrounding the equal sign is bigger than for the other aligning environments, rendering the document somehow inconsistent. This nice article from Lars Madsen explains (and illustrates with examples) why eqnarray shouln't be used anymore: [Avoid eqnarray!][1]


  [1]: http://www.tug.org/pracjourn/2006-4/madsen/madsen.pdf