In order to install .ipa files manually without using iTunes you need to patch MobileInstallation file on the iPhone iOS 4. The best way to patch the MobileInstallation file is by using the AppSync which will allow you to install apps on your Jailbroken iPhone 4 or iPhone 3GS without using iTunes.
The latest AppSync 4.0 is just released by the developer and you can follow the steps given below:
1) Start “Cydia” on your iPhone.
2) Tap on “Manage” tab on the bottom.
3) Now tap on “Sources” as seen in the screenshot below
4) Tap on “Edit”, and then on “Add”. You should now be asked to enter a url source as viewed in the screenshot below. Type “http://cydia.hackulo.us” and click on “Add Source”.
Cydia will now automatically update your sources by following a series of automated steps as shown in the screenshots below:
5) After installation is finished. Search for “AppSync for OS 4.0” in Cydia and install this application. This app will automatically patch mobileinstallation file on your iPhone or iPod touch running firmware 4.0.
If every thing followed as described then you will now be able to install .ipa files manually on your iPhone 4 and iPhone 3GS.