This is a big topic mate.
Gee were to start. In general terms "terorism" is a huge problem for shiping world wide. international piracy is the worst it has ever been costing somewhere in the range odf hundreds of millions to possibly billions of dollars every year, including insurance. AFAIK it is common practice for all freighters to lock the whole ship down when passing through the Malaka streights because the chances of being boarded and robed, or taken hostage are so high. However this is not being conducted by politically or religously driven "terrorists" but rather organised crime that is out to, and regularly achieves, a huge profit. I read that the major hot spots such as the malaka streights are run by "cartells" which cruise companies pay protection too. Thankfully they are not out to do as much damage to international commerce as possible so to a large extent this problem go's unoticed by the wider communiy. This may have a silver lining though, because if a religous or political group intended to start commercial terrorism in these area's they would have to displace these organised crime groups which would be nie impossible for someone like Al Qieda or Jimah Islamia. Such a turf war would definatly draw the attention of the powers that be so this is highly unlikely.
As far as a threat to Australia, to be honnest i'm not sure how this threat could materialise in reality, even if there were well funded and determined organizations intending to do us damage in this way. The simple fact is they need their own ground to launch such an campaign from, and there isnt too much of that within a realistic radius from vulnerable infestructure. As far as our lines of comunication with the US, Asia and Europe, the only real threat comes from areas were piracy is allready prevelant, such as the several streights through the indonesian archipelago and some south pacific islands. Basically any organization that intended to use these area's as a base to launch a campaign of hijacking or politicaly motivated piracy would face some serious problems. Lets take the south pacific for as an example, as it probably offeres the best opportunities for an terrorist organization, considering how crowded and populated indonesia is. For one thing they would need some significant infestructure (as far as a terrorist organization goes) within range of the sea lanes. They need vessels, men fuel & weapons, and i doubt there would be too many possible targets within a realistic area. This means they wouldnt be to hard to find and would have to deal with all of the firepower the ADF could come knocking with. Best case an SASR troop in the dead of night, at worst a battalion group with air and naval support. :shudder. If they deside to combat this with a smaller, less concentrated structure then they wont have a significant effect on Australian maritime trade. in essence in order to achieve their goals and significantly disupt Australian commercial tradde, they they would need enough capability to achieve that goal, which would make them prime targets for the ADF. Thats a battle they have no chance of winning.
As for our oil/natural gas infestructure: First, any form of large scale terrorist attack on a oil platform would have to come from a meduim sized vessel, which limits the options for potential terrorists. Naturally said infestructure in the southern ocean is alot safer than those in the timor sea. Ofcource a boat could drop off an "attack" force to attempt to take an oil platform in Bass streight, however it wouldnt get far before being boarded or sunk, or indeed being foiled before hand. Anyway these structures are very hard to take by amatures, even if they are undefended. It would be close to being unfeasable in anything other than a calm sea state. A single, pin prick attack is possible in the southern ocean, however it is no less likely than an attack on a major population centre which would be more productive for a terrorist group. Timor Sea oil/Ng platforms are alot more vulnerable, due to the proximity of foregin soil that could be used to harbor a terorist organisation. However there are also significantly more defence assets in the area. RAAF MPA aircraft, UAV patrols, Armidales and customes vessels are regularly in the are which means as soon as the terrorist vessel entered our EEZ, especially in an area with significant infestructure they would have to aviod detection and interception which would not be an easy task, especialy once we aquire global hawk as part of AIR 7000 (probably). A single armidale would pretty much end any terrorist attcak before it begun, and if they proved too much for an armidale to hande, then i'm sure it wouldnt take too long for a pair of Hornets to show up and put a couple of 1000lb Paveways down their smoke stack, which would end the show quick smart. In addition to this i'm pretty sure TAG west would has trained and is capable of putting a team onto an oil platform in a matter of hours. Anyway such an organization would have to be based somewere in indonesia, which is hardly a heaven for terrorists. JI has been ver effectively targeted by indonsian police, and putting together an operation of this size would not be easy. I guess what i'm trying to say is its possible but its not at all easy for a terorist organization to pull off. They would have serious problems in all phases of their operation, from their base of operations, to penitrating our EEZ to taking the platfomr to escaping (if they intended to). Again their money and time would be better spent attempting to insert a sleeper cell through "classic" technices and hit a civilan population centre.
Destruction of fishing vessels, well, they would need their own vessels which could be intercepted by RAAF fast movers within a reasonable distance. If mines were to used then this would be a conventional, government scale, type of threat, and would be dealt with accordingly. Any nation in the region who attempted this would have to deal with the wrath of the RAAF, which for most is not an attractive option. If a terrorist organization did posess the technology it would still have to penitrate our EEZ and acsess our shipping lanes, which isnt easy. A single vessel would beable to put 3 or 4 mines in the water, which does not constitute a major threat. The more vessels, the higher the attenetion level and the harder the operation would be to pull off. All this is reliant upon said terrorist organisation possesing the means to do this, technologically. And finally attempting to put operatives onshore would not be an easy task. We do have miles of unprotected coastline. However all of it is hundreds if not thousands of kilometers from major population centres. In addition to this problem it is some of the most inhospitable land on the planet. Surviving the remorte kimberly region, traveling to your intended target would be a remote possibility. Again, flying an operative in on a commercial flight would be ceaper, easier and have a higher chance of sucsess than attempting to insert them covertly by sea.
@ Octopus.....
The ammount of Biological agent and explosives needed to make this feasible is well beyond most terrorist organisations (i think and hope). The container itself would have to be the weapon because as soon as it was unloaded it would be discovered, unless you hid them in pots or statues or something, like many drug imports. But then you limit the size of the weapon.
As for sinking a ship in a shipping lane like melbourne harbour, its a realistic idea and would put a dent in the countries marritime trade for a while, and it would also not bee too hard to pull off. However a single shipwerck could be cleared up in a matter of weeks and shipping could be diverted to other ports and the goods transpoted by road andrail to the affected city. It would have a significant economic cost but i doubt it would be devistating. A coordinated attack on several major ports would be much more destructive. However this would be hard to achieve. You would have to have said vessels in critical choke points (i can only think of 2 places in melbourne and port philip bay that would significantly effect the ports turnover) at the same time in different states. This would be so hard to achieve because this would not be under your controll, but the harbour master and pilots. As soon as a single attack took place, all shipping would be halted and searched. So really only a single attack is feasible.
Sorry for the novel everyone but its a big topic...