Though I could write a whole article about the snake eating its tail, and how we come to rely on bots, I won't. Instead I'd like to play Sherlock and work the current EVE-Uni scandal backwards.
How He (could/should have) Did It
90% of what he could have used is absolutely legitimate. If you put in the effort, you too could build something similar in most regards.
Live Price Data: EVE Market Data Relay (EMDR)
It's EVE-Central on steroids. EMDR provides a direct feed from the as-it-happens uploads of market logs. This allows you to write a semi-live interface that can provide the shotgun of data required to really transcend the EVE market interface. By hooking this feed into a website or app, you would be able to watch wide swaths of the market with legitimate data.
Market Tricks: Little Known Tips
TL;DR, between a few keyboard macros and splitting stacks/orders on the market, it's possible to make a lot of changes very quickly. Split it further where you stack windows and alts, it would be pretty easy to legitimately script some of the more basic market commands. Protip: the scroll-wheel increments prices by a penny-per-tick
Here's where the operations get murky. Technically, none of the above techniques interfere with game data. By using EMDR + some keyboard macros, it would be technically simple to make the macros pretty intelligent.
The problem really starts to arise as you vastly outstrip "normal human" bounds... and averaging updates at 2s/update, I would really hope some klaxons went off for CCP Sreegs.
Where He Went Wrong
After reading the ever expanding story, it looks like he additionally used EVE cache files to achieve his goals. This is a no-no. After Bacon ran afoul using similar game data,
CCP made it pretty clear that using game cache files was off limits(correction and further analysis can be found here).
Love CCP's response or hate it, the simple truth is live game data is off limits. The client is sacred, and unless it comes with a straight export feature, or appears in the \My Documents\EVE\ folder, you have no business messing with that data. As long as in-game mods remain off the table, coming anywhere near the game client (without legitimate path) is a dangerous affair.
Also, I would like to praise CCP Sreegs for his team actually tracking those outside "normal human" operating limits. It's a fine line to be able to crack down on those representing the outliers without showing your hand as to what you justify as hunting criteria. As soon as people know the criteria, it's pretty easy to tune your bot down to fly under the radar.
A Note For CREST
This is the dangerous precipice CCP must tread carefully with CREST. Given the right tools, EVE will become the playground of bots, completely pushing out humans from large swaths of the game. And though us developers dream of AUTOMATING ALL THE THINGS, there is a lot of harm that can be done if humans are removed completely from game mechanics. This is why I try to keep my head down about suggesting new CREST features; because my suggestions are largely self-serving, and I can't even begin to comprehend the damage that could be done to the wider game.
There are a lot of excellent articles coming out of this scandal. I'm a little ashamed to throw my hat in the ring next to some of these: