I feel the first two qualify. The only ones that actually say 'Prototype' on the glasses are the 0.2p/0.3p's which are in reality just athlete samples. However, I guess, unlike the Green Camo Monster Dogs, or other colorway variations, these were test runs of the non-frosted orbitals and even had the gen 1 circular design while the frosted had moved to the gen 2 before the final polished finish which only came in the flattened design.
Since our hand is somewhat forced in that regard, I personally would only consider something a prototype if it was directly related to functioning as a decision piece. For example my Flying Tiger Oil Rig was used as a test canvas for the design, and once approved, they mass produced a similar pattern on the Gascans. Takumi also did pretty much the same thing on the Concept Studio, but those weren't meant to lead into anything else, so I wouldn't call those prototypes. However there were some that he painted and didn't result in a retail pair, but perhaps if they were used to consider a larger run (even if they didn't), that would still count. All about intent, which makes for some huge grey area.
The Clear Thump would be another good one. Aside from being used in the promotional material, it was used as a visual aid during the Thump's development (at least according to Jim when he posted on the now defunct thumpinfo.com)
Obviously the printed CAD models would count since rapid prototyping is about as exact as you can get. Sometimes they would also only print parts that change since many times new models build directly off an old one. For example the Jawbone started as a switchlock Classic Racing Jacket. Then it moved to a switchlock Straight Jacket II, so they only printed the orbitals but just snapped on the Jacket stems since those were plentiful.