I recently beat Sentinels expansion and enjoyed all of it but was a little disappointed about how short it was.

I never did many random encounters and I'm wondering if S3 has any special encounters like the ninja/katana encounter in N. Britain or the UFO in Switzerland and where they are located.

There's a little info here. I'm sure some of the people here and on the Nival boards can give more detailed descriptions as well.

Not really enough info. I've heard about the bank mission being kind of "special" and I found the downed V2 rocket mission which gives you little joe arrows, but does anyone have a list (with locations) of any other "special" missions like there were in S2?

There aren't many special missions that we're aware of (and even the random encounters are only of a few types):

I will add all types of encounters as I get them reported.

Special random encounters:
Shade's prison in Switzerland (middle of map) (two scoped and two normal rifles - guards in towers)
Bank robbery in Germany (bottom right corner)
Something in Egypt (haven't gotten that one yet)

Normal random encounters:
UK - underground bunker (downed V1 rocket, small structure above, little joe arrows in bunker)
UK - garage/repair facility - three buildings (basement garage connected with another building above ground - contained boobytrapped locker if I recall correctly)

Germany - train depot (one variant has MG mounted on flattop wagon) (some rifles/smgs, extra unarmed engineers)
Germany - generator facility (enclosed in wire fence, one variant has two motorcycles with sidecars, one with MG) (lots of enemies, several rifles)
Germany - large two-wing house with park and fountain.

Russia - small two-room hut with outhouse
Russia - houses with barn
Russia - road bridge (mostly pistols)

Poland - factory with flatbed truck.

Egypt - ruins with a cistern
Egypt - barren rock valley