Thankyou for all the responses so far. You've all given me plenty to work with, and yes I can see how my personal spending, goals and lifestyle affect which program and card would suit me best.
I suppose generally I was wondering about obvious pitfalls in the programs generally (as pointed out- beware expiry dates) or even between programs. Ie: Do certain programs have inbuilt advantages or disadvantages in comparison to one another or is the only real difference one of personal preference? Do people select VA because of loyalty or simply because they prefer that airline or is there something inherent in their programs/points accumulation/redemption that differs to Qantas.
I am still feeling my way through all of this, so my own goals aren't currently solid. I know that I want my rewards to be in regards to travel and I'm more than willing to pay the remainder or top off points through cash. As for whether I prefer upgrades or free flights or hotels- to me, money saved on any leg of the journey is worth it no matter the specifics. So, points towards accommodation don't seem any more or less appealing than points towards the flight in theory. I suppose it comes down to the specifics: for instance I have read that redeeming points on non economy class flights can be more difficult.
If you are talking mainly about 'domestic' programs, I'm not sure there is a lot of difference between VA and QF and I can't see any 'pitfalls' in one or the other. You can earn and burn on both types of flights to most destinations. I think QFF has more 'non flying' points earning opportunities, and they have more lounges around Australia outside the major ports. But people do have their airline preferences and then its a pretty easy choice of what program to join, notwithstanding it may not have every feature they would want.
QFF also has the advantage as it gets you into the international OneWorld Alliance and to me that is a huge advantage over VA Velocity, notwithstanding VA has quite a few codeshares and other international alliances.
If your horizon is more internationally focused, then for me its definitely a matter of global alliances and where you will probably want to use your points for (eventually). For instance, if you think you'll be flying within continental Europe (as opposed to to/from), then Star Alliance is definitely stronger, especially towards the east. To/from Nth America and Europe both Alliances probably suffice, but on the trip to/from Europe, I think there would be more Y+ and J seat opportunities on Star Alliance with SQ, TG (ex Australia) and LH, TK once you get to Asia - but maybe that point is debatable and SQ is definitely miserly with J Award seats. QF and EK are notoriously difficult to get Award J seats if you don't have status. Don't know about CX or BA.
For myself, even though I cough about them a fair bit, I can't imagine not being on QFF and I do enough work flying that I easily maintain WP status and have LTG (Life Time Gold), notwithstanding I know that AAdvantage is probably a better scheme with all my travelling to Nth America. With several of the USA schemes you can buy points to 'top up' to get to a flight Award points level, so if you want to fly 'free' # sooner rather than later, look for those.
I also belong to Air Canada's scheme, Aeroplan (Star Alliance) which I joined when my clients started flying me to Canada on Air Canada. But I learned the hard way that its an atrocious scheme. I've been meaning to move to UA's scheme, notwithstanding the airline I think is carp.
I've read that Aegean Airways (Star Alliance) makes getting to Gold level with the least flying, so if you want status (lounge access), then use them rather than SQ.
# NOTE: One definite difference between certain airlines and therefore impacting their schemes are 'fuel fines' on 'Award' flights. Qantas has high fees, as does Singapore, LH and in fact most airlines. But a few don't - United comes to mind. of course you can belong to KrisFlyer and get an Award flight on UA, but if you go Star Alliance why not join the UA scheme over Krisflyer, and you can buy points too?
This also impacts on whether you go for a J Award seat or Y. if its Y on Qantas, often the fuel fines will be almost the cost of an economy ticket!! So going for a J seat is definitely preferable.
Sorry there's no cut-and-dried answer, but I hope that helps.