[XPERIA X10 Themes and Apps] saltorio:
Hmm... because I ran it yesterday (as the script in one of my previous recent posts), and the following are still in the /system/app directory on my phone:

AccountProvider (.apk & .odex)

AlarmClock (.apk & .odex)

AndroidSyncService.apk

AndroidUI.apk

ApplicationsProvider (.apk & .odex)

AutoSettingsDispatcher (.apk & .odex)

Browser (.apk & .odex)

Calculator (.apk & .odex)

Calendar (.apk & .odex)

CalendarProvider (.apk & .odex)

Camera (.apk & .odex)

CapabilitySetupReciever (.apk & .odex)

CdfInfoAccessor (.apk & .odex)

Contacts (.apk & .odex)

CredMgrService (.apk & .odex)

DigitalClock (.apk & .odex)

DownloadProvider (.apk & .odex)

DrmProvider (.apk & .odex)

EManual (.apk & .odex)

Email (.apk & .odex)

EnhancedGoogleSearch.apk

FaceRecognition (.apk & .odex)

Facebook.apk

FileCopier (.apk & .odex)

Fota (.apk & .odex)

GlobalSearch (.apk & .odex)

Gmail.apk

GmailProvider.apk

GoogleApps.apk

GoogleCheckin.apk

GoogleContactsProvider (.apk & .odex)

GooglePartnerSetup.apk

GoogleSearch (.apk & .odex)

GoogleSettingsProvider.apk

GoogleSubscribedFeeds (.apk & .odex)

HTMLViewer (.apk & .odex)

ImProvider.apk

LatinIME (.apk & .odex)

LearningClient (.apk & .odex)

Maps.apk

MarketUpdater.apk

MarketProvider (.apk & .odex)

MarketUploader.apk

MediaProvider (.apk & .odex)

MediaUploader.apk

MediascapePluginManager (.apk & .odex)

MetadataCleanup (.apk & .odex)

Mms (.apk & .odex)

Music (.apk & .odex)

NetworkLocation.apk

PNPWizard.apk

PackageInstaller (.apk & .odex)

PcCompanionInstaller (.apk & .odex)

Phone (.apk & .odex)

Phonebook (.apk & .odex)

PicoTts (.apk & .odex)

ReadSdCard (.apk & .odex)

SemcCameraApplication (.apk & .odex)

SemcIME (.apk & .odex)

SemcSetupWizard (.apk & .odex)

ServiceMenu (.apk & .odex)

Settings (.apk & .odex)

SettingsProvider (.apk & .odex)

SetupWizard.apk

SnsContactImageCache (.apk & .odex)

SoundRecorder (.apk & .odex)

Stk (.apk & .odex)

Street.apk

Talk.apk

TelephonyProvider (.apk & .odex)

TimeScapeProvider (.apk & .odex)

TtsService (.apk & .odex)

UserDictionaryProvider (.apk & .odex)

Vending.apk

VoiceDialer (.apk & .odex)

VoiceSearch.apk

VpnServices (.apk & .odex)

WebMediaProvider (.apk & .odex)

Wiper (.apk & .odex)

Youtube.apk

bootinfo (.apk & .odex)

btoppservce (.apk & .odex)

generic-app-installer.apk

gtalkservice.apk

mediascape (.apk & .odex)

se-support-rachael.apk

semc-backup-rachael.apk

uWlopProvider (.apk & .odex)

Whereas the list of files on /apps on my SD card are much shorter:

AndroidQuadrapop.apk

au.com.phil.abduction.zip

battery.battery.zip

com.android.aldiko.zip

com.dataviz.docstogo.zip

com.paypal.android.p2pmobile.zip

com.quoord.tapatalkpro.activity.zip

com.td.zip

EManual (.apk & .odex)

LatinIME (.apk & .odex)

LatinIMETutorial.apk

Launcher (.apk & .odex)

moxiermail.apk

officesuite.apk

org.koxx.pure_calendar.zip

playnowarena.apk

se-support-rachael.apk

SemcIME (.apk & .odex)

SEMCTouchPalChinese.apk

SEMCTouchPalKoreanQWERTY.apk

trackid.apk

-edit-

Oh wait, now I see (looking back at my delete command). All the apps I specified were indeed backed up then deleted, and the .apk and .odex files left on the phone (in /system/apps) are those still installed. I get it now.