Indeed. Take it this way, as an example:
If you have installed and used Firefox for a while, and got bored of it, you might want to delete it. Simply drag it to the Trash, empty it, and it's gone from your computer. This is, as far as the majority of the people have to worry. But it's not true.
In ~/Library/, where ~ is your user name (to find it in Lion: in Finder, go to the menu item "Go" > Go to folder... > type in: ~/Library/) you find a lot of files. In the example of Firefox, it could be for instance your bookmarks.
Just a couple of kilobytes of bookmarks, maybe some settings you tweaked, add-ons you installed, and so on...
You can search for it and delete it individually, by dragging those files to the Trash and empty it, but it doesn't do much anyway. Just a matter of kilobytes, that's all. For this example, let's decide you don't remove those files.
Half a year later, when you decide to re-download Firefox to use it again, maybe because a newer version is available which is faster and better, you open up Firefox for the first time in a long while.
Because you saved all those little Library files from Firefox, all bookmarks you had, all settings you changed, and all things you did to personalize your Firefox experience are there, as if you never deleted Firefox from your computer. It can save you a lot of trouble configuring all settings again, just by not removing those Library files.
But then again, if you think not to use Firefox ever again, and want to regain those precious kilobytes, you can delete it without hesitation or harm. It's just preference files, that's all.