Q: cannot locate the applications that come with mac

They are in the Applications folder unless you've moved or deleted them. To replace them requires reinstalling OS X. You cannot download them.

By chance are you referring to those in the Dock?

iMovie and iphoto are attached to your Apple ID so you can reinstall them in the Mac App Store. Messages is a part of Mountain Lion not Lion.

If you purchased your Retina new only a few months ago then it came with Mt Lion. If you bought it used then those Apps might never of been reinstalled. So login to the Mac App Store and check in your purchases area.

Do this first and accept your free iLife, or if it's not available, it's been used by a previous AppleID and you will have to purchase it in AppStore.

Restoring your Free iLife (iPhoto, iMovie etc)

Upgrading OS X in the AppStore is now a free direct to Mavericks (10.9) which includes Messages.

You can avoid using Mountain Lion (10.8) entirely, it's likely not even there anymore to install.

So both are free for you.