I will try to hit your points one by one. Truthfully, I've been running OS X for almost 6 years and from my experience, I have not seen any degradation of performance over time. But for what it's worth, I am quite obsessive over the quality of my system, from performance to security, so this is an area I've actually researched and continue to have a thumb in. Even TRIM support for SSDs is a mixed bag.
- Run CCleaner to clean up all the crap (temporary files, hidden
caches, etc.) that browsers leave behind
While having orphaned caches and preference files won't slow down your Mac, some don't like leaving cruft behind as it can take up valuable HD space. Apps like AppZapper and AppCleaner remove these files and may be something you wish to take a look at. Personally I use AppZapper.
- Run CCleaner to clean the registry
Mac OS X does not contain a registry. All preference files (which house your personal settings) are located in your users Library/Preferences folder. Letting them accumulate over time will not have a negative impact on your systems performance (see above).
- Run AdAware to clean up tracking cookies, etc.
Again, this will not adversely affect a system's performance, but you are certainly welcome to keep Safari free of garbage. Personally, I use Jar to achieve this. It is quite good, but unfortunately has not seen an update in quite a while. However, it is the cleanest and simplest app (there are others, but they require 3rd party plug-ins that may hurt your systems performance and stability) in this department.
- Run MalwareBytes malicious software removal tool
Unnecessary on OS X. It has a native system to handle "malware" and while there has been only one documented case that has made it's way into the wild (with relative success), this still remains very much a non-issue on OS X. You can read more about the malware Mac Defender, and what Apple did about it. Malware remains a point of contention because it cannot be installed without some level of user interaction (unlike Windows).
- Run Microsoft's malicious software removal tool to backstop
malwarebytes (hoping that at least one of them would find the
Again, not necessary. See above.
- Run MacAfee's virus scanner (This piece-of-crap software never did
anything but give me headaches. But it's popularity made me
uncomfortable just deleting it)
You'll be happy to discover that OS X does not contain viruses or requires any utility to protect it from such threats. Do not be bought into the FUD by those that would have you consume resources by installing anti-virus software for your Mac (yes, some exist). The most common argument is that it creates a protective barrier that may not be that useful on OS X, but will prevent the spread to machines running Windows. This is a non-starter because all Windows systems already contain anti-viruse software to protect them, ergo, they do not require an additional barrier.
Not required. Apple has actually archived their document covering this topic as defragmentation and file optimization on OS X is no longer an issue. You can find it here. In a nutshell, it is not something a user should ever worry about. Disregard those that would have you install or copy your data to and fro in a vain attempt to "optimize" your files. OS X simply does not suffer from the problems that plague Windows in this department.