Given the Obama Campaign's admiral efficiency and operational acumen, I imagine the transition will also go smoothly. Good. It is a difficult time, one that has to be well-managed. The current President, whose transition period was marred by the whole Florida fiasco, managed to keep a disciplined eye on the importance of having a strong team in place...and he did just that.
The likely choice of Rahm Emanuael as White House Chief of Staff is an interesting one, and I have mixed thoughts about it. Emanuel is a hard charging, personally dynamic guy with a penchant for the politics of intimidation. You need a disciplined guy to run the White House, and Emanuel could be an inspired choice. He is also not close with Nancy Pelosi, something that lends hope to Conservatives fearing greater influence from the Speaker.
But Emanuel is also considered quite a harsh taskmaster. There are a lot of big egos in DC, and those big egos come attached to the big names President-elect Obama will want to have on his WH Staff and in his Cabinet. These kinds of folks (Lawrence Summers, Robert Rubin, Laura Tyson, etc) won't take Emanuel's crap. If he has matured since his bad boy days with the Clintons, he'll work out fine. If he hasn't, just wait for the fun leaks to come screaming out of the White House.