OK, although a fresh install is scary the first time, just make sure to do it in a methodical manner. There are multiple guides for how to properly do this so please google it if you plan on doing so but it is actually quite simple.
1. BACK UP EVERYTHING - use both time machine and superduper
2. Make a MANUAL backup on an external HDD of your really important things - Photos, Emails, Music, Contacts, Calendar, Documents, Downloads, Other Media, Bookmarks, etc - there are TONS of guides for how to do this
3. Make a list of all programs you install and make sure you have the files or discs to re-install them, if not get them now and back them up
4. After you are pretty sure you have at least 2 backups of everything that you KNOW HOW TO ACCESS, then start the process of reinstalling lion with a clean install.
5. Now, this is the toughie, and depending on your computer expertise you can always go to an apple store to help you with this one: Re-import all your data (emails, photos, contacts, calendars, documents, downloads, bookmarks, etc). Remember, each of the things has a different process to do it (ie itunes, mail, iphoto all have different ways to re-import the data which you can google) However, DO NOT USE THE MIGRATION WIZARD AS THIS IS PROBABLY CAUSING THE PROBLEM. When you use the migration wizard it will copy everything bit for broken bit, you need to avoid this to correctly install these files.
6. Once completed, you will need to manually install all non-mac app store programs (you can either use the discs that you have or re-download them if you bought them off the web, or re-install them from the downloads folder that you saved.
7. Redo all configurations for your apps (most painful part of process)
8. Hopefully it all went well and you have a brand spanking new machine free of digital rot.