Luke Wroblewski posted about Developing the Invisible, an interesting article where he explain the importance of alignment and whitespace in the user interfaces design, the invisible part in the design.

Padding, or whitespace, often fares worse. In some places, padding is gone; in others, there is too much. Padding is set to different values, leading to columns and rows of varying widths. Changes in padding and alignment can negatively impact readability and obscure visual relationships that clarify how to use an interface.

Figure 1 — example showing the difference between two designs by adjusting the invisibles

Figure 2 — Another example showing differences in padding and alignment

The two figure 1 and 2 provided explain very well the concept of invisible in webdesign, and its certainly one of the tasks that require lot of manual adjustments before finding the suitable alignment between the different user interface elements. Developping techniques and maybe tools will certainly help finding solution for the invisibles, for a given project this will take place certainly in the beginning and then a pattern could be defined to let the project follow in the same spirit.