You have to understand what an aircraft transponder does to understand the answers.
Mode A/C -Virtually all aircraft (including B1, B2, B52, F-22, F-35 etc) carry Mode A/C transponders. These work by a ground radar station pinging the aircraft, and the aircraft replies with a 4 digit (Squawk) code and/or an altitude. The Squawk is allocated by the controlling ground radar station, and the pilot dials in the code on the transponder. There is no tracking information transmitted by the aircraft.
Mode S : Most aircraft carry these - including all UK military types, European based F-15 & F-16's, C-17's, C-130's, KC-135's etc. These work by a ground radar station pinging the aircraft, and the aircraft replies with unique 6 digit hex code, plus stuff like speed, altitude etc. The hex code is unique to that aircraft on that day. Civil aircraft keep the same hex code for ever. Military aircraft tend to keep the same codes for a while, but some types 'rotate' codes from a pool of reserved ones (Lakenheath F-15's do this). There is no tracking information transmitted by the aircraft.
Mode S+ADS/B : Most civil types (airliners, biz jets), but very few military types carry these. Military types which do have the capability (RAF Voyagers, USAF KC-10's) often turn it off to avoid being tracked. With ADSB the aircraft does transmit it's Latitude and Longitude and so it's position can be plotted on a map.
Most of the tracking apps rely on ADS/B, so very few military types show up on them. The tracking apps also get forced to screen out certain types by the authorities if they want to use official ATC feeds. Air Force 1 is fully ADSB, but won't show on most tracking software.
It is possible to 'triangulate' Mode S only aircraft though. This works by groups of users all receiving the Mode S hex codes using their own recievers, and precicely timing the arrival of the signals (to sub-microsecond resolution). Then, given you know the speed of light, you can work out the relative distance of the aircraft from the ground stations. From that you can plot a series of arcs, and where the arcs intersect is the position of the aircraft. This technique is called MLAT.
IMHO the best app that supports MLAT is Planeplotter. There are others - ADSB exchange is one. However, the coverage relies on users contributing their own receivers input into the sharer system, so numbers of subscribers is critical.
AFAIK there are currently no apps that can track Mode A/C aircraft reliably. So B1/2/52's are a work in progress