8-Core 2.93Ghz 2009 Mac Pro - suddenly is s-l-o-w...

Question

Hey Guys - PC convert here, and familiar with the tools I would use to diagnose items that would cause a PC to slow down (spyware, malware, bloat, registry cracks, etc), as well as hardware associated with such, I am having a quandry with my 2009 8-core Mac Pro.
So, I noticed just the other day that doing menial tasks on my MP would take a few extra seconds, like clicking on the menu for it to show up 5-7 seconds later (when it was almost instantaneous previously), clicking on apps, going from one webpage to another, typing a post on the web (like this one where it would freeze up for 5 seconds), etc.
Not familiar with how I can diagnose what is really going on with my MP, I went into disk utility which took several moments to start up, and went to the disk that has the OS loaded on it (a Samsung 256GB SSD) to "verify" it. After checking it, it confirmed that the drive was corrupt, and guided me to repair it via boot disk (ie, put SL disc in, reboot, and disk utility it). I did so, and it gave me a confirmation that it had repaired the disk. Went to bed last night with a sense of satisfaction.
This morning, I booted up the MP, and all seems to run swimmingly. Then, I noticed late in the afternoon that it is starting to slow down doing these menial tasks again. Worried, I go back to the Disk Utility (which again takes 5 minutes to load) and do a verify on the disk with the OS on it. It confirms that the disk/volume appear to be OK.
So, now I am not sure what may be causing this. Based on my previous PC experience, this would either have been a bloated OS, spyware/malware, or a starting to malfunction hard drive. Since I am a noob to the Mac world, I am not that confident in diagnosing, so I am looking for help and tips on what I cna do to pinpoint the issue.
Here are some points I may have missed earlier:
1 - Ran a virus scan (Norton), and the scan shows no viruses
2 - I have two Samsung SSDs, 1 Rapter SATA, and 1 WD Caviar SATA drives connected. The other Samsung SSD and the two other SATA drives show up clean on the disk utility.
3 - Reinstalling OSes in the PC world is a dime a dozen when it gets bloated. Is that the same in the Mac OS X, SL world as well?
Any tips, hints, thoughts, suggestions, or guidance would be greatly appreciated. Thanks much!!!!!
sam

Answer 1

No, though maybe Snow Leopard could be different animal, cloning is a good idea, and only clean install if there are major bugs, crashes, corrupt files.
Every version of OS X has had an early buggy stage, intermediate which mostly works properly, and then, just before it is abandoned, it has its mature, stable working properly stage!
OS X can be run off of, and you can have, multiple boot drives, and easy to clone to a new drive (Casper 6 for Windows comes close to that). And SuperDuper (& others) do a good job cleaning or not copying the built up junk, that clean install isn't needed.
HFS+ isn't the greatest. It has gotten better, but without 3rd party maintenance tools, it will fail. And it is still a good idea to keep Windows handy to certify and map out bad sectors (or seems SMART Utility for OS X now does the job) but a vendor's own utility is best way to first format a drive. Apple First Aid will say "SMART failure" or find errors in the directory it can't fix; but it is the errors it doesn't see or look for or recognize that will get you - and your system.
Most issues are with the system drive. And you don't want to have to zero the drive twice a year, unless, like me, you want to clone and format a drive before copying; and because Apple formatting has changed and improved frequently with updates to Disk Utility.
A new OS (or mid-life) may involve new partition tables, in which case a new format may be best way to initialize. I am not a fan of letting an OS update attempt to update partition tables; not without backup, and I never apply updates without a couple backups (clone).
While Windows will spot and recognize bad/weak sectors and the need to run a chkdsk, I don't get the feeling OS X and HFS+ does, I/O errors instead go unreported or recognized.