I took the following steps to delete apps on iPhone permanently from my iTunes library. I use a MacBook Air and iTunes 11.0.04:

Open iTunes
Go to the Library drop down box
Select Apps
Click on individual app, press delete and hit enter
Confirm decision
Read more about iPhone Data Eraser here.

You should better seek help on iPhone-related forum.

Yes, I'm having the same issue about deleting apps from iPhone. I can't even delete them on my MacBook in iTunes. And on the old system, I could delete the Apple originated apps like Game Center and Stocks (for which I've never had a use).

Any help would be great appreciated!

Hi everyone,

Yesterday I tried to install a theme (AndroidPerfection0.6.zip). Everything was fine, until I created a "Categories" folder. Then I thought I was going to mess things up, so I deleted.

I respringed iPhone and some apps (Phone, Messages, Safari, App Store, etc) were crashing.

I deleted this file /var/mobile/Library/Preferences/com.apple.SpringBoard.plist and then my apps went missing (those which were crashing).

Then I start researching in the WinSCP and I had some shortcuts in the <root> folder. Such as bar, etc, and some other. /var now is inside /private (don't know how), and as I said, I have a /var shortcut in mz root folder.

Then I created a new folder in the root one, called Applications and I copied all the crashed apps. Respring, and they appear now, but crashed, all of them.

The ones that do not crash, are some apps inside /private/mobile/applications
And there are a couple of folders with names like 456JDSKFKSL35MDSJSD, and inside I have the Weahter Channel.app and some other folders. So this kind of apps, do lunch.

No idea what happened. I think I made a mess with copying and moving things. Right now I can't lunch some apps, they crash, and I don't know if this is because I have something like 3 different Applications folders, or if it is that the /var is not the mother folder but a shortcut, or what!

Can anybody help me?

I restore from previews backups, but nothing happened, the still crash. I don't want to restore from factory, as it will install the 4.1 firmware, and I don't think this one has been jailbroken already.
My WinSCP version is the 4.2.9
My Windows is Vista
My iPhone firmware is 3.1.2

Thanks in advance,
Tina