I don't take Sandringham or Frankston, but I can say that at rush hour you will be sharing the train with thousands of others. Sometimes it's standing room only (actually, it's often standing room only during rush hour). I don't know what time it starts but at 8am it's really really busy. During rush hour when I was taking the train into town I would say I was standing on the way in about 80% of the time, and on the way out, it depends on where you start. If you start at Flinders St, you'll get a seat because that's where the train starts. If you start at Parliament, it's already been going through the City Loop and you'll be lucky to get a seat.

They are air conditioned (dunno about all of them though) but when it's 40 degrees outside and you're bumping into people standing on a crowded train, no amount of A/C is going to help you. People fainted throughout the summer on trains (mostly elderly or infirm I think)

The trains are fairly reliable but the more crowded they are, the later they get. Expect to have a 5-8 minute delay during the height of rush hour. apart from that, they generally run on time.

As an aside, petrol in Melbourne has shot up to $1.70/litre, so more and more people are taking public transport. Some transport minister guy was on the news the other day complaining about how it's taxing the system (ironic, since they keep telling us they want us to use public transport instead of cars). So something to remember.