Does anyone know if when you transfer your Firefox backup files (the one in application data/mozilla/etc.), are the themes/plug-ins automatically transferred with the firefox files or will I need to re-download all my plug-ins/Firefox themes if say I wanted to transfer my installation of Firefox on a new computer? Basically do I need to bookmark all of my plug-ins/themes or will all of this get transferred with my firefox backup files?
Yep—extensions and themes are all contained within the Firefox profile folder. As long as you're transferring between the same OS, everything should be in order. A few links for reference:
Transferring data to a new profile - Firefox - MozillaZine Knowledge Base MozBackup - Backup tool for Firefox and Thunderbird FEBE (Firefox Environment Backup Extension)
Transferring data to a new profile - Firefox - MozillaZine Knowledge Base
MozBackup - Backup tool for Firefox and Thunderbird
FEBE (Firefox Environment Backup Extension)