Well this is for the newest rom 2.06.00 WWE. Release like a couple of weeks ago for Sprint PCS provider. Basically I used a CAB manger and extracted the files and looked at the registry and what ever file were included in the CAB. Basically this is an educated guess.

Also I installed the files one by one and see if my educated guess was correct or not. Sometimes I even used a Hex editor to view the files. I'm don't work in the engineering/software field at all but I'm really good with computers and stuff. Anyways here is my finding so you can decided what to leave in the custom extended rom. Any corrections let me know.
P.S. I only left 7 files for my customization and that gave me 39.86 MB of Storage Free.
RTPlugin_CDMA.sa.CAB
-Lets you have option of "set as ringtone" where it will copy the file to /windows/rings
ResString.sa.CAB
- Has something to do with HKLM\Security\ResOver with parm name 56. Replace Regcover
PT_Ril_Apac_206301.sa.CAB
-extract a file call rilphone.dll. Looking a the hex edit of it, seems like something involving the modem function.
PT_RemoveHTCBatteryICON_Apache_206300.sa.CAB
-Remove bottom right battery icon and remove title bar clock.
PPST_FILE_SPCS_1_19_003_with_PRL20224.sa.CAB
-The PPST cab actually updates the PRI . PRL (as you may know) controls what providers your phone will roam with. PRI, on the other hand, stands for "Product Release Instructions" and is essentially a list of settings for the CDMA radio. It is that updated PRI which contains settings to enable data roaming and to allow calls to interrupt an active data session (AKA "ring-thru"). (thanks luv2chill)
PP_Version_Apac_206303.sa.CAB
- Add in HKLM\SOFTWARE\OEM\3rdversion string MSYSTEM = 2.06.303 WWE which apparently makes a Item in Device Information called ExtROM with a description of 2.06.303 WWE
PP_LockUp_Apac_212705.sa.CAB
- Installs a couple of files; ohci.dll, qct.dll, qctusb.dll, rilphone.dll, SDemory.dll. Seems this is a fix/patch for various stuff.
PP_IOTA_v1_10_Apache_206300.sa.CAB
- Install something called jTelDll.dll. Has to do with IOTA.
PP_HTC_CM_Guardian_Apache_206300.sa.CAB
- Installs something called HTC_CM_Guardian.exe in windows directory. Not sure what it does but its installed in the startup menu so it run everytime you
restart the device. Has someting to do with SPCS Connection. Probably something to make sure that we don't mess up the SPCS connection settings.
PP_ErrCodeForSPCS_Apache_206300.sa.CAB
- Installs code translation. i.e. instead of Error Code 64 it will say "Unknown error. Sign in failed. Please try again. If the problem persists, turn your phone off then turn it on again."
IOTA.sa.CAB
- Installs for vision provisioning.
Enable_RingTone.sa.CAB
-Related to RTPlugin_CDMA.sa.CAB. Seems to give option to set midi, mp3, amr, etc for ringtones.
DirectShow.sa.CAB
- Has to do with windows media player. Seems to be associating avi,3gp,mp4,m4a,mid,midi,rmi,amr,awb,3g2,qcp with that program.
Customize_SPCS.sa.CAB
- Installs some sprint customization
Cert_SPCS.sa.CAB
- Install certificate
Cert_SPCS.CAB
- Disable the the security feature from asking permission to run a certain program
AudibleSample.sa.CAB
- Install sample audio files used by WTLAudiblePlayerPocketPC.arm.CAB
ButtonLock.sa.CAB
- Change button lock from Do not Lock buttons to Lock all but power.
Disable_RemoveProgram.sa.CAB
- Removes the various program i.e. AE, Goodlink, etc from Add/Remove Program
Fetch.CAB
- Install some with a picture of Action Info w/ today plugin
GetGL.CAB
- Install Goodlink
Getmail.ppc2003.ARMV4Rel.sprint.CAB
- Install the Sprint getmail
HiddenDurationPage.sa.CAB
- Hide the Call Duration page under Device Information
PhoneSetting_HelpFile.sa.CAB
- Adds PhoneSetting.htm help file and add Clear Voicemail Icon setting
PowerICON.sa.CAB
- Removes Bottom right battery icon.
sprint_software_store.CAB
- Install the Sprint Store Software
TimeSnyc.sa.CAB
- Makes it so that the time sync option is visable under Phone setting. Funny thing is that it's visable by default.
WTLAudiblePlayerPocketPC.arm.CAB
- Install WTL audio player w/ some skins