I never know how many stations to put on the transport rides. And when your first station is at the front of the park, would your peeps want to get on at the penultimate station, if it's not far away, and go back to the beginning?

Your guests do not see transport rides as "transportation" but merely as rides; so do not rely on such rides to carry people to other sections of the park. The overall length of the ride should not be more than 2-3 minutes (or guests will be complaining "I want to get off" even when only riding between two stations) and stations should be spaced about 20-30 seconds apart; also, to keep trains from bunching at stations (one train loading, another waiting outside ...even when you have set "leave if another train arrives" , which never seems to work), have one train for every two stations and use the block signal option - so four stations = two trains, six stations = three trains - now a train will not leave the station until the next station is empty.

Guests apparently ride randomly; they may get on at one station and off at the next, ride the entire route several times, or anything in between.

An interesting point, even if only riding between two stations guests will "experience" the entire ride, so events will count even if the rider doesn't actually go past them. I often use a monorail with five stations, the track loops out and back to the next station, roughly like a flower with five petals; place an event at the outer edge of each loop and a structure around each station. Excitement of around 6 is not uncommon, charge $4 - $5, and guests are lined up money in hand.

The best way to approach transport rides is to remember that they're more for your benefit than they are for that of your guests. If you want guests to show up in certain parts of your park without them having to use their own AI to walk there, that's when you build a transport ride. This is likely the main reason why they're the only ride type where 100% of guests completely ignore intensity ratings (you will never see them complain about going on "something more thrilling" even though the intensity is less than 1). As jgf notes above, they still only see them as rides--they won't get on knowing that the next station is near a roller coaster--so it's up to you to plan their fate accordingly.

I can't speak for RCT3, but in RCT2, guests always get off at the next station. So if your monorail has four stations--one at the entrance, one at the back of the park, one on the left side of the park and one on the right--guests will not be able to go between the front and back stations in a single ride. With those mechanics in mind, if you just want to transport guests from the entrance to the back of the park and back again, you're better off using Shuttle Mode rather than an entire circuit.

I'm only familiar with RCT3 Plat, and from riding the monorails, trains, etc. have noticed that guests apparently exit the ride randomly ...I've seen some ride the entire route several times, and some get off at the next station then walk back to where they were. And some will exit and get back in line for the next train.

"...guests completely ignore intensity ratings"
Probably because, at least in RCT3, none of the transport rides have intensity over 1. The fastest transport is the monorail, its top speed is a mere 17mph and has a track height limit of about 8; I've built one to go from the max height to as far underground as I could take it and it still only registered a max speed of around 24mph. No speed = no g-forces = low intensity; the only other option is to increase the ride length, and you will be getting "let me off!" complaints long before making an appreciable intensity increase that way. This negates using the mini-railway as most real parks do - a relaxing loop around the entire park.

In running shuttle mode my favorite ploy is to build two elevated stations (I prefer monorails since they don't use as much ground space ....and I just like monorails, lol) side-by-side at each end, the queue and exit lines extend from each side doubling back beneath the stations with the exit of one hitting the path opposite the entrance of the other; the tracks run parallel, with some curves added for interest. Running both in shuttle mode the trains met somewhere along the track, which seems to please the guests (if only there were some way to sync the trains so they would always be at opposite ends of the route simultaneously).

Too many of the transport rides in RCT3, unlike their real world counterparts, are virtually useless. The steamship is so abysmally slow that no one ever rides it; the elephant ride is popular but again so slow that you can't move enough people to be productive; for some reason no one ever rides the "water transport" (looks like speedboats) or airboats in my parks; and while the viewing galleries stay packed, even at $9 a shot, the safari rides through the same enclosures are lucky to get 100 people a year on them.