circles, triangles, and numbers
Train companies often have various types of trains. For the same train line, sometimes you will find subway-style seating along the walls, and sometimes the train will be set with normal pair seating. For these reasons, the car doors are not always in exactly the same place. To maintain the impeccable accuracy that Japanese transportation is famous for, these circles and triangles mark where the doors to the train will be when it stops.
The numbers indicate the train car number, especially handy if you're meeting a friend who is getting on the same train at a different stop.
Look up at the electronic signage to check whether your train's doors will open at the triangles or the circles, and then line up accordingly!
yellow lines with raised bumps
You'll find these kinds of yellow lines all over Japan; not just on train platforms but bus stops and sidewalks, too. These bumps are there to help the sight-impaired, and on platforms mark the safe distance to stand from the edge and occasionally where to line up for the train car doors.
To avoid the widespread problem of chikan, or perverts who harass women on crowded public transportation, most train companies have implemented a "Woman Only" car. These cars will be clearly marked on the train platform with a large pink sign. In general, women only cars are in effect during weekdays from 9 to 5. Check the platform markings for exact days and hours.