The different generators have their own advantages and disadvantages.
Could you please elaborate more on this topic? Just to make sure we are on the same page here ...
Here's my current understanding. It's subject to change, since analog circuits can work differently in the "real world" vs. theory.
Atmel CryptoAuthentication chipGood: Tiny, integrated solution. This means board layout is easy (no touchy analog sections to worry about) and device size is a bit smaller. It is very likely to Just Work.
Bad: As slush has pointed out, Atmel don't say how it works. They say it's "high-quality" but don't justify it. There's no access to the raw samples, meaning that it could fail to produce enough real entropy, though it still outputs seemingly random bits.
Thermal noise sourceGood: the existence of thermal noise is guaranteed by fundamental physics. The amplitude can be reasonably well estimated
a priori. The particular design used (a differential amplifier) rejects common-mode noise somewhat. Noise characteristics are simple (white, Gaussian).
Bad: requires a lot of gain, which can provoke oscillation. High-valued resistors mean that it's sensitive to parasitic capacitance; this can cause bandwidth, unwanted feedback or (external) noise feedthrough problems. Requires board space for 3 op amps.
Zener noise source from zener diodeGood: components widely available. Requires less op amps than thermal noise source. Noise characteristics are probably distinctive, which makes it easier to distinguish zener noise from everything else.
Bad: noise amplitude is tiny, requiring even more gain than thermal noise source. Noise amplitude probably varies between components, complicating mass production. While zener noise is generally unavoidable, most manufacturers strive to
reduce it.
Zener noise source from voltage referenceGood: Louder than zener diode. Probably more consistent than zener diode.
Bad: Once again, noise is usually unwanted by circuit designers, so chip designers try to minimise it. We had to look around for a chip which was noisy enough (the LM385 is used, which is an old chip). Voltage references aren't designed to be used as noise sources: they're designed to be used as voltage references. Slightly more expensive and bigger than zener diode.
Oh, I forgot this one: most microcontrollers have multiple independent oscillators (eg. crystal oscillator and internal RC oscillator). If both oscillators are run simultaneously, they will drift apart randomly. This drift can be measured using a suitable interrupt handler.
Drifting simultaneous oscillatorsGood: you get it for "free": no external components required.
Bad: uncertain quality of random bits. Throughput is quite slow - last time I tried, I was only able to get a few hundred bits of (unknown quality) entropy per second.
Some resources:
The zener noise source circuit we borrowed from:
https://mywebspace.wisc.edu/lnmaurer/web/minirng/RandomBit.jpgComparison of noise sources:
http://ciphersbyritter.com/RADELECT/MEASNOIS/NOISMEA1.HTM