I would say that it depends on what are you working on.
For example, when you're creating a renderer (software one), them keeping your memory aligned at 16-bytes and using SIMD SSE is a must (of course assuming you want to see some solid performance).
Creating a scripting lanugage and writing a code for working with that language - then it's most likely not worth it (as it won't speed you up at parts where you will be terribly slow).
Gimme few minutes - I will make some example code to show where memory alignment can help...
EDIT: Uhm... wanted to create some example, but I will link to one - http://www.cortstratton.org/articles/OptimizingForSSE.php - here you can see at some point that memory alignment helps, especially considering computations with matrices and vectors.