This question has been asked before many times, so you're not the only one wondering.
Here is just a sampling of answers for you:
Downtown Brooklyn looks to have alot of upside - with the NETS Arena, continued development, finishing up of the Cruise Line area, the Waterfront Park, DUMBO's continued awesomeness, Carroll Street, court Street and Smith really picking up quality stores, I really think that downtown brooklyn, Carroll Gardens, Park Slope, Boerum Hill, Cobble Hill, Ft. Greene, Clinton Hill, Red Hook and more have alot of upside.... If I was a buyer now, i would take advantage of the market situations and buy undervalued properties tha tare merey sitting due to buyer skittishness,
For a perspective, consider the 80's - everything seemed unattainable, people were losing their homes, interest rates were around 20%... yet smart investors bought homes, condos, coops, land, etc - and have now cleaned up. If you can buy something that gets an income or is undervalued, it is SILLY not to grab it. Especially in the NYC market, especially in Downtown Brooklyn, where the prices tend to be half of Manhattan anyway.
I always find it interesting that people can't see ahead a few years and see the potential in some of these areas, that are far from being fringe, and far from being risky. The commute to Manhattan from many parts of Brooklyn is comparable to the commute from the Upper East Side, believe me I know I lived there for 22 years - and in Brooklyn for the last 8.
A tip for NYC real estate is Public Transportation - buy property near major train lines that hit the Wall Street or midtown area, it will always be easier to Rent and Sell, in Brooklyn buy something with Parking! Remember I said 'near' not on top of, or next to - you should not hear the rumble of the train going by every 5 minutes....