Both seems to be gathering open data in a Wiki spirit, readable by machine and humans.
Freebase has existed for years, Wikidata is new.
"It looks like the main difference is two-way integration: instead of just scraping data from Wikipedia dumps to produce a structured database (like Freebase and dbpedia do), it's going to store the canonical version of some of the information there, and pull from it to populate the infoboxes. One of the motivations seems to be to keep the data in sync across Wikipedia languages, so an addition or fix propagates to them all, which is currently done somewhat awkwardly by a mix of manual and bot measures." by _delirium