The Case Against Customizability

Three words on building customizability in to your product: don't do it. This is to the products that allow users to change colors, organize panels, choose icons, etc.

Users have a hard enough time with finding functionality

Watch your technophobic family members try to attach an image to an email. While you may have no problem getting through menus to do it, they often do. Remember: there are more of them than us.
Customizability just gets in the way for super-users because they have better ways of doing it.

Your Product is a Tool, Not a Piece of Art

Your goal as a designer should be to minimize the amount of time on your software because it should just work.
Get your users back to the real world where they can go create art or enjoy it.

Troubleshooting/Documenting is Hard With Customizability

When you write tutorials, it is easy when everything is the same. Customizability makes it harder to follow tutorials, especially if the writer has a custom setup.
Users will also find it harder to help one another, which means more support is needed from you!

It Leads to Messy Code

Just think about rearranging components on the web, you need a place to save the information, a new server interface for submitting it, security procedures over that to make sure it isn't an attack vector, another library user-side to test in every browser.

Most of the Users Will Never Do It

Take BlackBoard for example, I TA a bit, and of all the students I've seen pull up blackboard, not one of them has changed the style or layout as they're allowed to; nobody wants to spend the time on a product they use twice a day.

Your time is better spent on usability

iGoogle was a great example of this, instead of needing a homepage like they used to, users can now just type what they want in to the search box and get information relevant to them.
Spend your time figuring out why users would need to customize, and eliminating that need.

Final Note

I'm not advocating that you throw everything in to code, no no! I fully support MVC, that is how superusers can change your environment to suit them best. If you must allow user tweaks to your software, like moving around menus, put it in a plugin so when your code gets updated, the whole software doesn't break.