As a result of this research, I was able to determine the following:
Ignoring application files, and ignoring the fact I do not have Phone installed on my BlackBerry, I used a visual diffing utility to determine differences:
Files that exist only in BlackBerryOS 3.8
FastEuropeanOptions
brickbreaker240X260resources
dynamic_ling_data_english_gb_35k_2
dynamic_ling_data_english_gb_ltr
dynamic_ling_data_english_us_35k_2
dynamic_ling_data_english_us_ltr
net_rim_bb_address_book_repository
net_rim_bb_backdrops_240x260
net_rim_bb_help_gprs_charm__en
net_rim_bb_profiles_tunes_builtintunes
net_rim_bb_resource__en_GB
net_rim_bluetooth
net_rim_er_enabler
net_rim_escreen
net_rim_platform_im_resource__en_GB
net_rim_platform_resource__en_GB
net_rim_theme_blackberry_240x260
net_rim_theme_tmobile_240x260
net_rim_tid
net_rim_tid_basicFastEuropean
net_rim_tid_core
net_rim_tid_fastEuropean
net_rim_tid_im_alph_core
net_rim_tid_multitap
net_rim_tid_repositoryBasedEuropean
Files that exist only in BlackBerryOS 4.0
brickbreaker240X160resources
net_rim_bb_explorer_resource__de
net_rim_bb_explorer_resource__es
net_rim_bb_explorer_resource__fr
net_rim_bb_explorer_resource__it
net_rim_bb_help_gprs__en
net_rim_escreen_common
net_rim_escreen_gprs
net_rim_midletresumption
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