The noise sources are not active during a transient analysis. You can get what you want using the PNoise analysis in SpectreRF. See sections 6.1, 6.3, and 9.1 in Predicting the phase noise and jitter of PLL-based frequency synthesizers, which can be found at http://www.designers-guide.com/Analysis/ for information on how to do this. With this approach, you would not view the noise using an eye diagram. Rather you would see the power spectral density of the noise sampled at the threshold crossing. This approach has two significant advantages over transient noise. First, you get the noise spectrum rather than just the noise power. Second, you can view the individual contributions of each of the noise source using the noise contributor summary.

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SpectreRF is useful for all kinds of non-RF circuits. Documents on this website show how to apply it to predict jitter of digital circuits (such as phase/frequency detectors and frequency dividers) and switched-capacitor filters. People are also using it for ADCs, switching-power supplies, and digital audio amplifiers.

It is really changing analog simulation.

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If the earlier comment about SpectreRF being a "harmonic" simulator refers to harmonic balance, the comment is not true. SpectreRF is a not harmonic simulator, it is a shooting Newton simulator, which is very different and makes SpectreRF a better option when devices produce waveforms with sharp edges.