I have binary matrices in C++ that I repesent with a vector of 8-bit values.
For example, the following matrix:
1 0 1 0 1 0 1
0 1 1 0 0 1 1
0 0 0 1 1
This is a bit late, but I just stumbled across this interchange today. If you look at Hacker's Delight, 2nd Edition,there are several algorithms for efficiently transposing Boolean arrays, starting on page 141.
They are quite efficient: a colleague of mine obtained a factor about 10X speedup compared to naive coding, on an X86.