You mean identification from inside the car or just looking at bare transaxles sitting outside the car?
Inside is a snap - if you see an overdrive on/off button (O/D button on shifter and corresponding indicator lamp on dash) - then it is a 4-speed automatic.
Just looking at the bare transaxles - easist way to tell is from the transaxle pans. If it got 15-bolts, it is the A131L 3-speed transaxle. If it has 18-bolts, it is the A145E 4-speed transaxle.
Here are some pics of the gaskets - to give you a quick idea of the shape of the pan.
3-speed
4-speed
Also keep in mind, that if you are looking for a swap - be mindful of the application. If the original car had a 3-speed, you cannot just throw on a 4-speed and expect it to work. You also have to grab the appropriate ECM from the donor car. Same with going from a 4-speed to a 3-speed or to a 5-speed manual - to avoid problems, grab the right ECM.