I back up my iPhone 4 and iPad 2 to iCloud. Is it necessary to keep my Mobile Applications Folder? There are over 12GBs of space being used by this folder on my Macbook. Could it be thrown out?
Hopefully this helps people in the future, it's ok to delete it locally from your Mac and it won't affect your iOS devices. Backup everything to iCloud and redownload from Apple Store. You can even do the same with iMovie and GarageBand (two apps I really don't use but take a bunch of space on my Mac Air 120GB).
Directly copied from iTunes below.
Are you sure you want to delete the selected apps from your iTunes library? These apps will not be deleted from any iOS device that synchronizes with your iTunes library.
Edit 2016-06-07: the behavior described here is no longer valid, at least for iTunes 22.214.171.124 and iOS 9.3.2 (both the most up-to-date at the time of this edit). It is completely safe to go into iTunes and delete iOS apps, they will not be removed from your phone when you sync. (Just tested this on my own phone.)
Original answer left intact below:
Do you sync your iPhone and iPad with iTunes (even occasionally)?
If the answer is no, you can go ahead and delete the iOS apps stored on your Macbook? If the answer is yes, you need to check if your apps get synced too while syncing your iPhone and iPad? If the answer is no, you can delete the iOS apps on your Macbook. If the answer is yes, you need to connect your iOS device to iTunes, click on your device in the column on the left, click on the 'apps' pane, and uncheck synchronising of your apps. The problem is that when you do that, the apps on your iOS device will be deleted and you'll have to redownload your apps on your device through the appstore. If you don't want to do that, you can choose to not sync your iOS device with iTunes anymore but that means you won't be able to sync anything (movies, tv-shows, ...) with iTunes.