I restored my Mac running 10.9 from time machine after a re-install but it appears that the symbolic links under /usr/local/bin for some of the formulas were lost.
/usr/local/bin
You can brew unlink and brew link for each app.
brew unlink
brew link
If its painful for you, you can back up from your timemachine "after boot".
If you import data from your timemachine at starting your machine, brew broken, but after you restart your machine once, it will work.