Long time lurker... First post. 8)
I've been a profesional EE in the semi industry for quite a few years now, I'm suspicious about those eye diagrams provided in the Inq story (and evidently in some mysterious white paper - anyone got a link to that?). IMHO, those eye diagrams are not what they claim.
1) Eye diagrams are usually taken over many thousands of cycles, these only look like they have a few hundred, as evidenced by the clear outlying traces.
2) For some reason, not all the traces start at the same point in time and/or voltage. I've never seen a scope or analyzer that would trigger/record like that. To me, those lines look like they were drawn with MacPaint or something.
3) The eye diamond shows a height of approx +/- 250mV = 500mVp-p, which would about match with the PCIE spec. What the Inq diagram does not show is that this eye also has a max voltage spec. Specifically, The PCIE spec has two eye diagrams, one for "de-emphasized bits", which specifies 566mV >= Vp-p >= 505mV; the other for "transition bits" specifies Vp-p >= 800mV. Thus the second graph showing the "good" eye would be failing terribly because it has a 700mV swing, and there is no way to tell if it's a de-emphasized bit or a transition bit.
A quick Google provides an excellent link with a diagram of what a real PCIE eye diagram looks like.
Textronix PCIE testing software
Finally, just to be snippy, the author clearly has no idea what "common mode" actually means, and seems to be pretty weak on the concept of jitter as well. Not to mention the sillyness of posting graph results and interpretation without any kind of experiment description. Just kind of pisses me off (enough to finally get off my lazy a$$ and post here).