From the NDepend website:
PercentageBranchCoverage: (defined for methods) Branch coverage is a more accurate measure of coverage than PercentageCoverage because it compensates for method complexity. Since branch coverage is generated from the underlying opcodes, it often does not map cleanly to source code. That means it’s difficult to take branch coverage values and determine how to write tests that will improve coverage.
Branch coverage is only available if your coverage data are imported from NCover or OpenCover coverage files and if the metric NbLinesOfCode is available.
Recommendations: The bottom line is:
Use PercentageCoverage as your measure of quality, but
Use PercentageBranchCoverage to determine which code statements need more testing.
It is also interesting to observe branch coverage values in conjunction with Code Source Cyclomatic Complexity values.