Customizing color schemes or other aesthetic elements of your web app provides users with an opportunity for self-expression. As such, it will be valuable for users who identify with your app. There are three classes of app where this may be the case:
Apps that are intended for self-expression (e.g., personal sites like MySpace and Facebook). If the purpose of the app is for the users to create representations of themselves, then you probably should support aesthetic customization.
Apps used in some sort of public performance or interaction. If others are going to see the users use the app, then it becomes associated with the users, and they may want to control their self-presentations. This includes companies that use your app and want to "brand" it as their own. PowerPoint slides are an example of this, but so are apps used in informal social situations (e.g., something used among groups of friends).
Apps that are central to an important and frequent task. If users invest their identities in their vocation or avocation, it may extend to the tools they use, so they may like to personalize them. If some of your users are real enthusiasts for your app (the way some are about Basecamp), then you may want to support aesthetic customization. Keep in mind that supporting aesthetic customization will not create enthusiasts for your product, but it can enhance the enthusiasm that is already there.
The above applies to a very small number of apps. Most web apps are used infrequently for a specific task that isn’t all that important to the user. Most users are about as interested in customizing the appearance of web apps as they are in customizing the appearance of their toaster oven. As long as it looks reasonably stylish and doesn’t offend, then users are not going to want to spend time futzing with it.
Aesthetic customization may also provide entertainment value to the users as they try different colors or styles and see the result. However, if your users are that bored with your app, you probably have more serious problems. You should try to find a better way of amusing them (e.g., with powerful advanced features that actually have utility).
If you do provide aesthetic customization, remember that most users are not designers and usually their customizations will be worse from both an aesthetic and usability standpoint than what you would choose. You can mitigate this somewhat by providing canned themes.