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1) Rarity. Ultimately how many were made, and the following will limit general availability:
1a) Length of production run
1b) Exclusivity of the set (i.e. exclusive to a retailer)
1c) Price (higher price = less made)
2) Exclusive parts (almost always minifigs)
3) Popularity of theme
4) Quality of design
5) Discontinuation of license/theme
A set doesn't need to satisfy all the criteria, but a couple will be enough to make it one of the stratospheric aftermarket sets.
1b) Lego exclusive: nowhere near the volume made and sold as common sets
1c) High price, particularly price to piece ratio, which further hurt original sales, IMO
2) Exclusive minifigs (duh)
3) Popularity of theme: Star Wars (duh, again)
Obviously people were collecting the minfigs then, as well, but it was nowhere as manic as the environment is today. Lego has defintely fueled the minifig craze by recognizing this phenomenon and starting to release exclusive minifigs with nearly every Star Wars set.
I should expand on the idea of "popularity of theme". In the case with licensed themes generally, and Star Wars, Batman specifically, you have a secondary group of collectors outside of Lego collectors that are adding to demand. I think this is less the case with Indiana Jones and other licensed themes.
Also, the length of time that Lego maintains a theme will help grow the fan base of that theme, and for fans coming late to a theme, there is a desire to collect retired sets. Unless Lego restarts Indiana Jones, I don't think it will ever reach the stratospheric levels of some other themes, but surely it will still be elevated.
1. A civilian scene, not very common in the city theme anymore.
2. A decent set.
3. A LEGO 50 year anniversary exclusive.
1) Aftermarket supply is low
By far the most important. I.e. how many are available. And this is mostly affected by something EOLing without much fanfare (Zombies), or simply going out of print without going on clearance first (Winter Bakery) or nobody realizing the true potential of a set while it was around (Winter Toy Shop).
2) It is globally popular
In other words, is the set's individual (or general) theme globally popular with the masses? Harry Potter, Monsters, Christmas sets, farm sets - these always seem to do well because people simply love them. I hesitate to include Star Wars simply because Lego SW is so damn diluted these days. For a Star Wars set to increase in value, it certainly can't rely on this factor alone.
3) It wasn't available forever
If a set has an overly long life span, especially if it has been discounted nicely and has some of the other magic factors in this list, then chances are people have gobbled them up for resale. Hello DS & FB! Note: Going against this particular factor won't necessarily prevent a set from increasing in value, but it likely will prevent it from skyrocketing.
4) The set is simply cool
This could be minifigs, parts, etc. but really, this alone won't get a set very far at all. Examples: PQ and Atlantis sets were very cool sets with fun playability and some of the best minifigs around, yet they languish because they didn't have any of the other factors in their favor.
5) It is part of a series
Being part of a series adds to the collectability, in that people gotta get em all. Sometimes this is a theme (Harry Potter), others an annual offering (Christmas sets, modulars) or other just a series (MBA). Also, the first in any series is likely the most desired because usually a series gets traction down the road, and by that time, the first in the series is no longer available.