It's understandable that this can happen. Plugins are generally designed to allow functionality without any template editing, and automatically including CSS and JS means that your plugin can look "right" to most users. However, we believe that plugins which include this kind of code should have "Developer Friendly" options, which allow you to turn off these includes and keep full control over how your site is styled.
A specific example: The PXS Mail Form plugin is a simple, light WP plugin which looks for
code and replaces it with, yes, an email form. It's getting rather old (last update was 2005), and there are mail form plugins with greater functionality, but PXS wins over the newer, flashier ones because of this simple feature:
It allows you to turn this extra CSS off.
Of course, a developer who's smart enough to know they don't want multiple lightbox.js versions embedded in their template or style declarations in their content is probably smart enough to also know how to hack it out of the plugin responsible, and we've done so on many occasions. This causes problems for upgrading though, we have to document these changes and remember to re-apply them whenever the plugin is upgraded, which makes more work for us, and more expense for our clients.
So, whenever we can, we try to use plugins which either don't do these "unfriendly" things, or give us the option to disable them. So this is a list of plugins we've discovered which are Developer Friendly: