Though applications usually do not take up as much space on your iPhone as the contents of the iPod section they can still weigh you down. They take up face space on the pages and an excessive amount can cause glitches and creates long periods of time searching for the applications you want. The best way to avoid this is to continually clear out old applications that you do not use and are just a waste of space. You can easily just remove them from the pages by pressing down on an app, holding it until all the application icons start shaking, and then hitting the little black and white X that appears in the upper right hand corner. Usually this just gets rid of it temporarily and often when you sync back to your iTunes it will reappear. Here is an easy way to both stop it from syncing again and delete it permanently.
Plug your iPhone to your computer and open up iTunes. When you are there select your iPhone from the Device list and then select the Applications tab in its section. When you are here, you will get a list of all the applications you have downloaded and still have. There will be a check box next to each one, and it will be filled with a check if the application is set to sync. All those without a check in the left hand box will not sync when you plug your iPhone in. Above this list will be an option to sync all applications or just sync the selected ones. Make sure that you are checked just to sync the selected applications instead of all of them. If you want to make sure a select application will not sync back to your iPhone just uncheck the box next to it.
If you want to delete the application completely you have to go to a different process. Go to the Library section in the left hand bar on your iTunes display. Find the Application section and select it. You will then see all of your applications will have icons on a large black plain. Here you can just right click the application you want to delete and select Delete, logically. Then it will ask you if you want to permanently delete it by sending it to the recycling bin. Hit Move to Recycle Bin instead of Keep Files and you will have finally removed that application.