Not sure where to start with your question, but I would suggest to look at a few things first.
If you regularly de-fragment and registry clean then how much free space is available on your hard drive? If you have less than 10% then Windows will not run smoothly at all and may crash the drive to the point where any data recovery is not possible by normal methods.
Games sometimes run faster when accessed from the Hard Drive than the CD but it depends on several other factors as to how effective this is, the free space on the Drive, the Graphics capability, the amount of RAM available and the virtual memory configuration amongst other things.
You can clear out the programs you don't use to create more space but if you have no idea what the programs do, then you should do a bit of research first and find out what the programs are for before binning them. JAVA you will need on-line, several features will use JAVA so don't delete it.
I take it you mean a complete system recovery, as in putting it back to factory default. You wont need to back up much except your documents, pictures and music as the programs that came with your machine will re-install provided you have either a recovery CD or a recovery partition. Extras like your printer software you will (or should have) discs for, plus things like Office and other 3rd party software not supplied by the laptop manufacturer. Any software you downloaded you will need to save the download file, print off any CD keys you may need (Windows, Anti Virus etc). You may want to save your Emails, depending on where your mail comes from and how you access it determines if you need to back it up (look in something Tools> Options>Storage Folders for the location), Hotmail, GMail, Yahoo mail and the like are generally stored on the server not your laptop.