[vedranm@inf2 ~/ns-3-allinone/ns-3-dev]$ uname -a
FreeBSD inf2.ffri.hr 9.0-BETA2 FreeBSD 9.0-BETA2 #0: Sat Sep 24 14:26:01 CEST 2011     root@inf2.ffri.hr:/usr/obj/usr/src/sys/GENERIC  amd64

sqlite3-3.7.8 is installed:

[vedranm@inf2 ~/ns-3-allinone/ns-3-dev]$ file /usr/local/lib/libsqlite3.*
/usr/local/lib/libsqlite3.a:    current ar archive
/usr/local/lib/libsqlite3.la:   libtool library file
/usr/local/lib/libsqlite3.so:   symbolic link to `libsqlite3.so.8'
/usr/local/lib/libsqlite3.so.8: ELF 64-bit LSB shared object, x86-64, version 1 (FreeBSD), dynamically linked, not stripped
[vedranm@inf2 ~/ns-3-allinone/ns-3-dev]$ ls /usr/local/include/sqlite3.h
/usr/local/include/sqlite3.h

However, configure ends with:
---- Summary of optional NS-3 features:
NS-3 Click Integration        : not enabled (nsclick not enabled (see option --with-nsclick))
GtkConfigStore                : not enabled (library 'gtk+-2.0 >= 2.12' not found)
XmlIo                         : not enabled (library 'libxml-2.0 >= 2.7' not found)
Threading Primitives          : enabled
Real Time Simulator           : enabled
Emulated Net Device           : not enabled (<netpacket/packet.h> include not detected)
Network Simulation Cradle     : not enabled (NSC library liblinux2.6.26.so is missing: NSC has not been built?)
MPI Support                   : not enabled (option --enable-mpi not selected)
NS-3 OpenFlow Integration     : not enabled (Required boost libraries not found)
SQlite stats data output      : not enabled (library 'sqlite3' not found)
Tap Bridge                    : not enabled (<linux/if_tun.h> include not detected)
Python Bindings               : not enabled (PyBindGen missing)
Use sudo to set suid bit      : not enabled (option --enable-sudo not selected)
Build tests                   : not enabled (defaults to disabled)
Build examples                : not enabled (defaults to disabled)
GNU Scientific Library (GSL)  : enabled