As "Tullamarine" mentioned, the viewing carpark on the Western side of the airport is probably the best if you have a Southerly or Northerly wind blowing. This will give you a side-on of aircraft using the North/South runway.
If you want to be directly under the aircraft or just off centre of the approach/climb, then you can stop down the Southern end of the field on the same road (near the Tullamarine golf course).
You can also stop just off Sunbury road on the Eastern and Northern approaches. The problems here are that you cannot see the airfield itself if that is what you require. Also, you will only see approaches from the East, as aircraft rarely take off this way.
If it does not matter if you get a bit of fence in the shot, you can possition yourself near the emergency gate on Sunbury road to the NE of the runway intersection. Just be mindful that whoever is driving the car makes sure they park to the side as not to restrict entry or exit in case of emergency. This possition will give you good shots of landings from the North, average shots of landings from the East, interesting takeoffs to the West and good takeoffs to the North.
My last suggestion is the road that goes around the back of the tower. You have to access the road via Keilor Park Drive (I think it is this road - the one that lines up with the Ansett Maintenence base). You turn off this road where the AN and QF staff carparks are (you will see buses frequently going to them).
It is a shocking road to drive on as it is uncealed, but you will get some fantastic footage of aircraft taxiing if landings are being conducted from the East.
I have flown out/in of MEL around 50-55 times in the last two years and not once used 09. I am kind of glad, because it would feel wierd approaching MEL from that side.
I find that you can get so used to something that when it changes it feels really odd. I am also one of those types who subconsciously knows the landing sequence at most major airports in Australia, and when things happen differently it can be quite unnerving. There is nothing worse on approach than when you look out the window expecting to see something and it ain't there