When apple says "we backup EVERYTHING" what exactly is everything?

Question

I am recently having minor issues with my mac (undetected clicks, laggy or weak video (expose) and many others, nothing too annoying).
I am aware that computers slow down after some time because the installing and uninstalling of applications and the downloading and deletion of files can leave behind some random bits of data that slow the computer down with time.
So I was planning on backing up with time machine, re-install OS X so that i would have a clean, freshly installed system. But if time machine backs up EVERYTHING, doesn't this mean that these corrupt bits of information are being backed up too? and wouldn't this mean that restoring from the time machine backup would bring those bits back and bring the issues back with them?
thanks in advance

Answer 1

It isn't random bits of data that aren't removed being the issue.
Most OS X applications are distributed and installed as a bundle. A bundle contains all of the components for the application in a single folder that is represented by the application's icon.
When starting an application, a preference file for the application is created, which stores the application's preference settings. With an application like the Mail.app, the application's preference file stores all email account information in addition to application settings. An application's preference file takes up very little hard drive space if not deleted. For the most part, when deleting an application that is distributed as a bundle, moving the application's icon to the Trash, along with the Application's preference file, and emptying the Trash removes all bits associated with the application.
If an application is installed with an installer, and not via drag and drop, an un-install utility is usually included and required to remove all application bits when removing the application. Most Microsoft applications install bits spread out all over the hard drive.
The problem lies with a hard drive becoming increasingly fragmented over time, which isn't nearly as much of an issue with OS X as it is with Windows.
http://docs.info.apple.com/article.html?artnum=25668
Installing and removing applications, adding and deleting data, regularly working with large video files, regularly burning data to CD or DVD media over a period of time fragments the hard drive.
Before performing an Erase & Install, check this link which may be helpful.
http://www.thexlab.com/faqs/performance.html
Someone else may have a differing opinion, but if it were me, I would backup my important data, perform an Erase and Install, run Software Update, and then re-install all 3rd party applications. I would then restore my data from my backup, such as my Mail.app data, documents, iTunes library, iPhoto library, Address Book contacts, and iCal Calendars.