This question asks if Voyager suddenly encountered unexpected gravity from an unseen object, how would it be detected, and there are several answers.
For the farthest probes - those now farther from the sun than Neptune - how are (or have) precision trajectory measurements
actually been made? I'm looking for a concise answer with links. Of course more info is always welcome, but I need one or a few "punch lines." For example "ranging by means of timing of a coded pulse train transmitted from earth, received by spacecraft and rebroadcast on a different frequency" (question and answer) or "doppler shift by means of same" or "apparent position by VLBI".
I'm not looking for "well for example you could..." type of answers in this case, just how
actually it is, or has, been done.
With velocity anomalies measured via doppler on the scale of milli-Hz mentioned here by @JohannesD, I'm guessing the doppler measurements are not based on an internal, high-precision clock in the spacecraft because the remote timebase stability could always be called into question, but instead rely on retransmission by each spacecraft of a ground-based signal, with some clever way possibly to change frequency/band in a precise way.
For reference only, here are some related hypothetical items: visible imaging, and infrared thermal imaging are ruled out quantitatively for this question. Ranging is mentioned here and here as well.
From the image below (from here) I count five spacecraft now past Neptune, four of which are using 1970's technology.