[Desire Q&A, Help & Troubleshooting] mindfik83:
I always remove unwanted .apks from the downloaded .zip file / custom rom prior to install.

You should use 7zip (Freeware - Google it) to open and browse the files in the .zip and delete the unwanted .apks. Everytime I have tried with WinRar it messes up the .zip file (wont install!), only works for me with 7zip (may work with Winzip too but untested by me).

The .apks can usually be found in sd-ext\app_s\ - depending on the rom you are installing.

N.b if your rom has the directories customize\app\ - don't delete the .apks in there as they are for the setup at rom install, are are selectable via the setup/install menu, deleting them may break the setup from completing.

Many .apks are deletable for example - I delete most widgets as I use a different launcher after install so they are useless to me.

e.g

com.htc.htcmsgwidgets3d.apk

com.htc.Sync3DWidget.apk

HtcAutoRotateWidget.apk

HtcDataRoamingWidget.apk

MMS.apk is the text message app and is deletable if your going to install something in its place after install. An example would be GO SMS.

Same with browser.apk - its the browser app. I delete it then after rom install I install something like Opera, Firefox or Dolphin etc.

DockMode.apk is for if you use a dock to connect your phone to your PC or car holder. I have neither of these things so I delete this.

Music.apk is the music player, and if your gonna replace it with another music player (Poweramp or Winamp for example) or simply dont want a music player, then is deletable.

MySketcher.apk is a touch drawing app which I dont use, so I delete that.

For me Titanium Backup PRO is a very useful program for uninstalling native .apks from the rom after install. Works perfectly.

If I forget to delete some native .apks I go into it, uninstall a load, then from the menu select -> more -> Clean up the Dalvik cache and it cleans up any stuff left that relate to the native .apks I have uninstalled.

There are many lists that can be found via google or here on XDA, but I have found many to be wrong. I worked out wot I could delete with trail and error.

Takes a while, but then you find out exactly what you can and cant ditch.

For sake, here is a list I have complied and have edited based on my knowledge of removing .apks prior to removal, some may or may not apply to you rom.

SHOULDNT REMOVE:

AccountAndSyncSettings.apk -> needed for Gmail Notifications

Calendar.apk -> Calendar

CalendarProvider.apk -> Calendar Provider

Camera.apk -> Camera

CertInstaller.apk -> Certificate Installer

Contacts.apk -> Contacts

Contacts.apk -> Contacts provider

DefaultContainerService.apk -> need to install apps

DownloadProvider.apk -> managed Downloads

DrmProvider.apk -> DRM provider

Fonts.apk -> system fonts

OmaDmcClient.apk -> OTA function can not simply be erased

Phone.apk -> Phone App

Settings.apk -> Settings App

SettingsProvider.apk -> Settings Provider

TelephonyProvider.apk -> Phone Provider

UserDictionaryProvider.apk -> Dictionary

Vending.apk -> Google Market

DeskClock.apk -> disables the alarm function

FmRadio.apk -> if the radio function is no longer needed

FmRadioProvider.apk -> if the radio function is no longer needed

GoogleCalenderSyncAdapter.apk -> Calendar Sync

GoogleContactsSyncAdapter.apk -> Sync Contacts

GoogleFeedback.apk

GoogleServicesFramework.apk -> provides account / login information for Google

CAN REMOVE

AnalogClockWidget.apk

AppAdvisor.apk

BatteryUsageWidget.apk

BookmarksWidget.apk

Browser.apk

Calculator.apk

CalendarWidget.apk

CarHome.apk

DeskClock.apk

DigitalClockWidget.apk

EmailWidget.apk

FriendsPlusWidget.apk

GalaxyWallpaper.apk

Gallery3D.apk

GenieWidget.apk

Gmail.apk

GoogleQuickSearchBox.apk

LiveWallpapers.apk

LiveWallpapersPicker.apk

MagicSmokeWallpapers.apk

Maps.apk

memo.apk

MessageWidget.apk

MusicWidget.apk

News.apk

PhotoAlbumWidget.apk

PhotoFrameWidget.apk

PolarisOffice.apk

VisualizationWallpapers.apk

VoiceSearch.apk

WeatherWidget.apk

:)