[...]perhaps someone can explain the differences to me?
I am wondering which one should I buy to a silent home rig...
The differences in the degree/decibel tables are probably from two different test rigs. The "small" coolers take on the 1155 platform and the "large" ones the 1366, i.e. a 95 W TDP CPU or a 130 W TDP CPU. This brings us to the big question: what are You
Unless it's some crazy overclocked monstrosity from yesteryear, I doubt either cooler would have trouble keeping the CPU cool and the fan RPM low. What you really want to check out in this case are the verdicts on the coolers' stock fans, in case you're not interested in swapping out for a personal favourite or an all-round champion. What caught my attention in the fan verdicts were these two tidbits:
SPCR on the 120 mm version wrote:
Interestingly, the F12 is not equipped on any of Noctua's other coolers, nor has its design been carried over to any of their larger fan models. The F series may simply have been a short-lived experiment that has reached its conclusion.
SPCR on the 140 mm version wrote:
At 7V / 940 RPM it's generally quiet and smooth but there is an audible scratchy sound as if some kind of fabric is rubbing up against it slightly. This artifact is fairly soft-sound though and is thus preferable to the typical tonal issues that plague most acoustically-challenged fans. As the speed is decreased further this oddity starts to fade and is replaced with a faint hum.
To summarise, the 120 mm version seems to have died out, and probably for a good reason (+1 for the 140 mm). The 140 mm does have its quirks, but seeing as you're going silent, your RPM will be low and the character most likely not a problem (+1 for the 140 mm). HOWEVER, the 140 mm is probably more expensive, and it is naturally larger and heavier (+2 for the 120 mm).
My opinion: go for the 140 mm if you can afford it, it fits into your setup (case, mobo, RAM), and the heavier weight is not an issue. We'll see if it's pure overkill when we hear what your setup is, though.
I've recently helped build two mITX rigs with the 120 mm version and no complaints so far, but I haven't heard either one live myself.