weighttp(HTTP負荷ツール)をmakeする際に軽くハマったのでメモしておきます。
C_INCLUDE_PATHを指定するだけです。

# C_INCLUDE_PATH=/usr/include/libev ./waf configure
Checking for program gcc,cc              : ok /usr/bin/gcc 
Checking for program cpp                 : ok /usr/bin/cpp 
Checking for program ar                  : ok /usr/bin/ar 
Checking for program ranlib              : ok /usr/bin/ranlib 
Checking for gcc                         : ok  
Checking for library ev                  : ok 
Checking for header ev.h                 : ok 
Checking for library pthread             : ok 
Checking for header pthread.h            : ok 
Checking for header unistd.h             : ok 
Checking for header stdint.h             : ok 
Checking for header fcntl.h              : ok 
Checking for header inttypes.h           : ok 
'configure' finished successfully (0.356s)