Download MyBackup Pro from the marketplace and back up everything to the SD card. For saving your app list I prefer using AppBrain. Then go to Setting>Privacy>Factory data reset. It will do a clean wipe of the device. When you restart you will need to reprogram your phone and go through the original setup screens. I would avoid setting up verizon's backup Assistant (it's redundant and uses up battery). I don't use HTC's version of facebook, twitter, flickr, either so I don't set up those apps either.
After all that you need to download MyBackup Pro again to your device then you can pick and choose the data you want to restore. It has an option to restore your apps, but it just provide links to them. I prefer using AppBrain to back up my app list. I would also not restore settings as the whole point of the reset is to start all over with new settings.
Tips:
If you have some apps that you loaded outside of the marketplace make sure to store a copy of them and have them clearly labeled. If you're using the Swype beta save the installer apk and then you can run it again and it will ask you to log in with your registered email and will download and install the beta again.
I found that restoring the HTC Sense home screen scenes restored fine, but took a very long time. I would clean up only the scenes you need and delete what you don't need to reduce the number of them and making that process faster. Remember that most of your widgets probably will not work so you have to reinstall them to your home pages after installing the apps to your device. Program links should work fine again after reinstalling the apps, so you shouldn't have to recreate the links for those apps on your home screens (the associations with be re-established after rebooting your device).
Contacts restore can also take a long time if you have a lot, so I prefer just syncing all my contact with my google account and restoring by re-syncing with my google account vs restoring from SD mybackup pro.