Try to follow this steps to compile cowpatty-4.2, you can find  last version 
here.
I've succesfully compiled under Windows XP SP2 with 
cygwin and winpcap.
First step it's to install 
cygwin, make sure that you check to install gcc, cc, stdlib, openssl, etc, default installation will work.
Dowload from 
here winpcap win32 dll libraries and install it on windows then get and unzip 
WinPcap Developer's Packs , copy headers files from .\include\* to c:\cygwin\usr\include\pcap and libary file from .\lib\* to c:\cygwin\lib\ .
Check that you've correctly installed winpcap dll by open a cygwin session (double click on c:\cygwin\cygwin.bat) and type which Packet.dll wpcap.dll.
Administrator@notebook ~
$ which Packet.dll wpcap.dll /cygdrive/c/WINDOWS/system32/Packet.dll /cygdrive/c/WINDOWS/system32/wpcap.dllDownload and extract cowpatty-4.2.gz.
tar xsvf cowpatty-4.3.tgzEdit Makefile, add path for pcap headers
old file:
##################################
LDLIBS          = -lpcap
CFLAGS          = -pipe -Wall -DOPENSSL
CFLAGS          += -O2
LDLIBS          += -lcrypto
new file:
##################################
LDLIBS          = -lwpcap
CFLAGS          = -pipe -Wall -DOPENSSL 
CFLAGS          += -I /usr/include/pcap/ -I /usr/include/
CFLAGS          += -O2
LDLIBS          += -lcrypto
Now It's time to compile:
Administrator@notebook ~/cowpatty-4.2
$ make
cc -pipe -Wall -DOPENSSL -I /usr/include/pcap/ -I /usr/include/ -O2  -g3 -ggdb
-c -o md5.o md5.c
cc -pipe -Wall -DOPENSSL -I /usr/include/pcap/ -I /usr/include/ -O2  -g3 -ggdb -c -o sha1.o sha1.c
cc -pipe -Wall -DOPENSSL -I /usr/include/pcap/ -I /usr/include/ -O2  -g3 -ggdb
-c -o utils.o utils.c
cc -pipe -Wall -DOPENSSL -I /usr/include/pcap/ -I /usr/include/ -O2  -g3 -ggdb
-c -o cowpatty.o cowpatty.c
cc -pipe -Wall -DOPENSSL -I /usr/include/pcap/ -I /usr/include/ -O2  -g3 -ggdb
-c -o genpmk.o genpmk.c
That's it.

If you have any problem please let me know.
vf