You have greatly expanded a simple question.
If you want more powerful tools check out Norton Utilities , Disk Warrior.
The AppStore,Macworld, and Cnet are good sources.
Onyx mentioned in previous post does many things.
Onyx has several cautions in its documentation.
Disk Tools is safe unless you interrupt it while running.
Vis a vis many of the things in the extended quote they apply to the OSX server.
I use web mail that eliminates one problem.
Missing icons get replaced eventually through self healing.
Improper uninstalls and installations cause this also.
Software developer are not created equal.
That is why many are not on AppStore.
They do not follow guidelines.
Big name commercial products have their own guidelines many times.
OS X does fsck and rebuilds caches on boot. ( cache cleaning) ( Checkout Kext Wizard)
Be aware if you want to do more than disk tools you will need commensurate knowledge.
"Danger Will Robinson"
Good sources are Apple User forum,Apple Developer site, Darwin, and Mach Kernel.
You seem to have a lot of Windows experience.
With Windows you do need a host of tools just to keep machine from blowing up on a daily basis.
This is not the case with a Mac or Hack. ( registry editor cleaner etc. , driver zombies )
You said you have backup. Be sure to check out Carbon Copy Clone or SuperDuper.
You should at minimum have a separate partition that runs,preferably a separate drive.
I have had a Mac since MacPlus. Although I am aware of some problems along the way I have never sat around worrying like the 'rant' posted. I am sure this person loved Clint Eastwood and the empty chair.
The rant brought up many topics each which would need a lengthy dedicated thread.
The emphasis at Tonymac is on installation and hardware, but there is an Infinite loop section to handle Apple and third party SW.
General techniques
Turn off auto updates.
Only use standalone downloads of updates.
Update only when necessary.
Wait on downloads until they have been run through the ringer at this site.
Ignore comments such as 'worked for me ...no problems' ( updates )
Look at comments such as ' this hosed my system it messed up X,Y, and Z. I fixed it by doing this ' ( updates )