By all accounts, the Jedi Temple was a storehouse of vast amounts of information. Holocrons, books, and the like. What became of this after Order 66? Did the Emperor take control of it? I've never seen any of its contents mentioned in any of the EU books I've read. I'd imagine there was tons of useful information that he would want to take hold of. Was it destroyed? Stolen? Sold? Something else?
Many of the holocrons (particularly the Sith Holocrons the Jedi had captured over the years) were taken by Darth Vader after the events of Operation Knightfall. In the novel Dark Lord: The Rise of Darth Vader,
Vader would be sent back to the Temple by his master in order to retrieve the Sith holocrons stored there. Vader knew this to be a test of his will, if he could pass through the Force-imbued Temple without succumbing to the horrors wrought there he would be commended. Vader was accompanied by Head of Imperial Intelligence Armand Isard whose men had detected a hacker in the Archives. Vader suspected that it was Purge fugitives Roan Shryne and Olee Starstone. While Isard got a location for the two Jedi, Vader wasn't able to get to them before they slipped away again.
Though it doesn't give any more information, Wookiepedia notes that:
With the Temple largely cleared of all valuable information by the Dark Side Adepts, the Empire maintained a small presence to maintain defenses in the event of a Jedi intrusion.
Some of the holocrons remained at the temple, as seen during Starkiller's (Galen Marek) trials, while others were taken by Palpatine for relocation.
Perhaps one of the most important parts of the temple, however, was the Jedi Archives, which survived partially intact, though after the fact hackers were able to delete small portions of its data (mainly records of particular Jedi's existence).
the surviving Jedi turned their weapons and Force abilities on the Stacks themselves, destroying countless centuries of information. However, the Sith had the upperhand, managing to slay all the Jedi and save several shelves of data. Once the Temple was secured, Vader turned the data over to Darth Sidious, who entrusted Armand Isard to recover any valuable data from the shattered font of information and history.
Notably, the Great Holocron was thought to be taken by the 501st Legion for Sidious at this time.