I can't see my applications

I cannot see my files in several folders on my PowerMac running 10.9.1. Specifically the Application folder seems to be empty, but a search reveals the files and folders are there.  How do i 'unhide' them?

Mac Pro then, the PowerMac line G5s can't and ended in Early 2006 run at highest 10.5.8.
It sounds to me like your directory was/is very damaged and while now 'repaired' not sure how much faith and trust I would put into it.
You ought to keep bootable backups so you can restore, in addition to TimeMachine which you can boot from and restore with.
Carbon Copy Cloner can make an exact copy of your working system. I recommend two, one from pre-Mavericks or befofe you make an update. Also, to do a file integrity check on all files copied using checksum. And it does a smart update and can include Recovery partition.
A lot stronger and as I said I woudl not rely on Disk Utility alone. Fixing the directory does not insure or say anything about the state of or integrity of any files, or the health of the disk drive and its sectors.
Clone your system:
How to Clone a Volume
Using Cloning as a Backup Strategy
See also Erasing a Drive, How and Why to Partition a Drive, RAID.
http://www.macupdate.com/app/mac/7032/carbon-copy-cloner
Using Cloning as a Backup Strategy
http://macperformanceguide.com/Mac-HowToClone.html

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