The brief rattle that katekebo describes as the first type has been present to some degree in almost every vehicle I've owned. Our '11 Rav4 does it too. It's never been accompanied by any rough running though and maybe lasts less than a second. I've always considered this normal for most internal combustion engines.
That's correct, although it is more noticeable in some engines than others. The only engine I had that was completely rattle-free (and was the smoothest, quietest, totally vibration-free and had the best torque curve from 1000 rpm to redline) was an in-line six BMW. This engine was, by far, the best engine I ever owned.
Toyota engines in general tend to be noisy, rattling and somewhat rough. They are reliable and durable, but they not particularly refined. And they are only middle-of-the-pack in terms of performance (torque/power per displacement and fuel economy). Toyota tends to be fairly conservative and usually stays one generation behind manufacturers that lead engine development (Mazda, Honda, Ford and the Europeans). The result is that Toyota engines are usually free of "growing pains" associated with introduction of new technologies, but have only average performance specs.
The 1AR / 2AR engines in the RAV4 and my current Venza are probably the most notorious offenders in terms of rattling, noise and vibration I ever owned. I had GM, Nissan, Ford, VW, BMW, Renault, Suzuki and Kawasaki (motorcycle) vehicles. I think all of them were generally "smoother" than current Toyota 4 cyl engines. The only engine that rattled even more than the Toyotas was the Kawasaki motorcycle engine, but this was a totally different animal, designed for performance, not comfort (with 13,000 rpm redline, lol). I found Nissan to be probably the most refined (and quietest) engines in the mainstream / budget category.
Every manufacturer follows somewhat different philosophy. Toyota is all about reliability and durability. Mazda, Honda and the Europeans are about class-leading performance. BMW, Mercedes are about "you can have it all" - performance AND quietness AND smoothness AND durability.