While I'll admit to not having looked at the actual write-ups, I'm a bit dubious about calling anything with a one-word name a "Prestige Class". I might accept the D20Modern term "Expert class" for such things, but (as far at T20 is concerned) I'm firmly in the camp that believes that Prestige classes are all about being noteworthy, not just being a specialist...
Also, as T20 actively encourages multi-classing, one of the (far too) common PrC practices in D&D of using a PrC to make up for the perceived weaknesses of multi-classing is simply not justified in T20.
An ideal set up as far as I'm concerned is to provide a continuum of increasing specialization and noteworthiness. To borrow the above mentioned classes as an example, I'd love to see Commando and Sniper written as "Expert" classes that basically require a level of Army or Marines (or equivalent, but tough to get elsewhere) and be startable *only* during active military service if you use that service as the prereq. If you meet the "non-service" set of pre-reqs, you can take the classes any time. These would be short classes representing the special training of those specialties.
Now, we look at the Traveller background and decide whether or not there are elites among these specialists. The militaries of the Imperium have millions of snipers and commandoes scattered across the stars, but there are only two hundred Ilelish Black Shadows at any one time, and *everyone* has heard of the Crown's Own Sharpshooters...
Similarly, every Imperial citizen knows of the Ministry of Justice, the Imperium-wide "police", but few are aware of the existence of the MoJ's "Special Branch".
Leaving the Imperium, we have the Zhodani Tavrchedl', also called the Guardians of Morality, or the "Thought Police". This strikes me as a good candidate for the "Expert" class type, specializing in detection, analysis, and rectification of unhappy thought. Are these hard-working mental custodians a "Prestige" class? There are literally millions of them in the Consulate, and they are by definition either Nobles or Intendants already. More significantly, is their training sufficiently complex that it requires immense skill (ie. high level and lots of skill ranks) to even begin the training, or are they "simply" specialist telepaths that can have their training represented fully by adding a skill or two to the character's permanent class skill list and tacking on a feat or two? Sounds like an Expert class to me.
Now, if there were a seniority and experience based group within the Tavrchedl' known for a particular reputation, or whom the years have brought unique psionic talents to ("welcome to the Million Minds Club. You will be inducted into the Gestalt this evening.") then there might be a PrC in there as well...