Well, I'm partial to the "Miser's Funeral" between Gribn and Thehir (sp?) - in the Hatuli system, I believe. The main reason I prefer this run is that because there's no jumping involved, you can complete a run very quickly (both in terms of days and in terms of playing time). Unless you've captured all your escorts, it definitely matters how many days it takes to complete a run because you're paying for them each day.

The way I compare trade routes is by totaling the profit from each item bought and sold, and then dividing this by the number of days the trip takes (including landing/take-off). This gives me a comparative profit in terms of credits/ton per day. That tends to be the best measure of how fast you can make money. I don't have exact figures available (I'm away my Mac), but I remember that the "Miser's Funeral" is one of the most profitable because it takes only 2 days to complete a circuit.

By comparison, the weapons trade route to Emalgha is pretty mediocre because it takes so long (in both days and playing time) to complete one circuit. Sure, you can make 2000 credits/ton from one run, but in the same amount of time you could have completed the Miser's Funeral something like 20 times and made far more profit. It's an issue of quantity - how many times and how quickly you can make the small sale versus the profit from one big sale. (Honda is far more profitable than Ferrari).

As for danger, you can do the "Miser's Funeral" in a cargo transporter - it has enough speed to avoid most of the opponents you'll run into if you zip directly to the other planet and don't stop to fight.