AFAIK there is no problem mixing and matching different timing RAM: system will run at the speed of the slowest module.
I don't think anybody will notice the difference with CAS latency Coot'ing and Refmac'ing.
I don't think there is much sense in having more than 4 GB of RAM per physical core on a Mac.
Majority of the Mac flock does not really care for where the RAM modules come from.
As for Mac Pro's- they use ECC RAM with proprietary heat sensors, so that's a completely different story. You can still use generic ECC RAM in a MAC PRO at the cost of the fan being stuck in hurricane mode.
The bottleneck of pretty much any modern system is the HDD. Apple-branded HDDs were known to have somewhat modified firmware, causing problems at times (mostly with AppleRAID, if not using an Apple-branded HDD)
An end user most definitely will notice an SSD VS HDD, which brings up TRIM support on OS X, which is limited to controllers sold by Apple.
Upgradeability-wise Apple is not the way to go in any case.
DISCLAIMER: The rest may be much more inflammatory.
Personally, I am not convinced OS X and Apple is the way to go log term (having been surrounded by MACs for the past 4-5 years)
I am not happy with the direction OS X is going. Too much emphasis on eye candy and not enough on underlying technology.
ZFS (long ago), Xgrid and X11 have been ditched, which I find disturbing. I don't see Apple investing in computers given current revenue from that sector.
Linux in a virtual machine of your choice might be a better bang for the buck. Or, Windows in a virtual machine on a Linux box for that matter.
Don't kick me,
DIR