diff --git a/Makefile.am b/Makefile.am
index ba196cc9..88880608 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -37,5 +37,5 @@
 ACLOCAL_AMFLAGS = -I m4
 
 # Subprojects
-SUBDIRS = libguac guacd
+SUBDIRS = libguac guacd protocols/vnc protocols/rdp
 
diff --git a/configure.ac b/configure.ac
index 3d0c795a..10c81e95 100644
--- a/configure.ac
+++ b/configure.ac
@@ -43,7 +43,7 @@ LT_PREREQ([2.2])
 LT_INIT([dlopen])
 
 AC_CONFIG_MACRO_DIR([m4])
-AC_CONFIG_SUBDIRS([libguac guacd])
+AC_CONFIG_SUBDIRS([libguac guacd protocols/vnc protocols/rdp])
 AC_CONFIG_FILES([Makefile])
 AC_OUTPUT
 
diff --git a/protocols/rdp/Makefile.am b/protocols/rdp/Makefile.am
index 595691f8..a4864469 100644
--- a/protocols/rdp/Makefile.am
+++ b/protocols/rdp/Makefile.am
@@ -37,7 +37,7 @@
 AUTOMAKE_OPTIONS = foreign
 
 ACLOCAL_AMFLAGS = -I m4
-AM_CFLAGS = -Werror -Wall -Iinclude
+AM_CFLAGS = -Werror -Wall -Iinclude $(LIBGUAC_INCLUDE)
 
 lib_LTLIBRARIES = libguac-client-rdp.la
 freerdp_LTLIBRARIES = guac_rdpsnd.la
@@ -93,6 +93,9 @@ endif
 libguac_client_rdp_la_LDFLAGS = -version-info 0:0:0
 guac_rdpsnd_la_LDFLAGS = -module -avoid-version -shared
 
+libguac_client_rdp_la_LIBADD = $(LIBGUAC_LTLIB)
+guac_rdpsnd_la_LIBADD = $(LIBGUAC_LTLIB)
+
 freerdpdir = ${libdir}/freerdp/
 
 EXTRA_DIST = LICENSE
diff --git a/protocols/rdp/configure.in b/protocols/rdp/configure.ac
similarity index 83%
rename from protocols/rdp/configure.in
rename to protocols/rdp/configure.ac
index e21c6713..937b675f 100644
--- a/protocols/rdp/configure.in
+++ b/protocols/rdp/configure.ac
@@ -34,26 +34,39 @@
 #
 # ***** END LICENSE BLOCK *****
 
-AC_INIT(src/client.c)
-AM_INIT_AUTOMAKE([libguac-client-rdp], 0.7.4)
-AC_CONFIG_MACRO_DIR([m4])
+AC_PREREQ([2.61])
+AC_INIT([libguac-client-rdp], [0.7.4])
+AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 
-# Checks for programs.
+LT_PREREQ([2.2])
+LT_INIT([dlopen])
+
+AC_CONFIG_MACRO_DIR([m4])
+AC_CONFIG_SRCDIR([src/client.c])
+
+# Programs
 AC_PROG_CC
 AC_PROG_CC_C99
 AC_PROG_LIBTOOL
 
-# Checks for libraries.
-AC_CHECK_LIB([guac], [guac_client_plugin_open],, AC_MSG_ERROR("libguac must be installed first"))
+# Libraries
+AC_CHECK_LIB([pthread], [pthread_mutex_init],, AC_MSG_ERROR("libpthread is required"))
 AC_CHECK_LIB([cairo], [cairo_create],, AC_MSG_ERROR("cairo is required for drawing instructions"))
 AC_CHECK_LIB([freerdp-cache], [glyph_cache_register_callbacks],, AC_MSG_ERROR("libfreerdp-cache is required (part of FreeRDP)"))
 AC_CHECK_LIB([freerdp-core], [freerdp_new],, AC_MSG_ERROR("libfreerdp-core is required (part of FreeRDP)"))
 AC_CHECK_LIB([freerdp-channels], [freerdp_channels_new],, AC_MSG_ERROR("libfreerdp-channels is required (part of FreeRDP)"))
 AC_CHECK_LIB([freerdp-utils], [xzalloc],, AC_MSG_ERROR("libfreerdp-utils is required (part of FreeRDP)"))
 AC_CHECK_LIB([freerdp-codec], [freerdp_image_convert],, AC_MSG_ERROR("libfreerdp-codec is required (part of FreeRDP)"))
-AC_CHECK_LIB([pthread], [pthread_mutex_init],, AC_MSG_ERROR("libpthread is required"))
 
-# Check for libvorbisenc
+
+# If bundled copy of libguac found, use that
+if test -d "$srcdir/../../libguac"
+then
+    AC_SUBST([LIBGUAC_LTLIB],   '$(top_builddir)/../../libguac/src/libguac.la')
+    AC_SUBST([LIBGUAC_INCLUDE], '-I$(top_srcdir)/../../libguac/include')
+else
+    AC_CHECK_LIB([guac], [guac_client_plugin_open])
+fi
 
 have_vorbisenc=yes
 AC_CHECK_HEADER(vorbis/vorbisenc.h,, [have_vorbisenc=no])
@@ -71,16 +84,19 @@ else
     AC_DEFINE([ENABLE_OGG])
 fi
 
-# Checks for header files.
-AC_CHECK_HEADERS([guacamole/client.h guacamole/guacio.h guacamole/protocol.h freerdp/locale/keyboard.h freerdp/kbd/layouts.h])
+# Functions
+AC_FUNC_MALLOC
+AC_CHECK_FUNCS([memset socket strerror fork])
+
+# Headers
+AC_CHECK_HEADERS([freerdp/locale/keyboard.h freerdp/kbd/layouts.h])
 
 # Check for FreeRDP version-specific features
 AC_CHECK_MEMBERS([rdpPointer.SetDefault, rdpPointer.SetNull],
                 [], [],
                 [[#include <freerdp/freerdp.h>]])
 
-# Checks for library functions.
-AC_FUNC_MALLOC
-
+# Done
 AC_CONFIG_FILES([Makefile])
 AC_OUTPUT
+
diff --git a/protocols/spice/configure.in b/protocols/spice/configure.ac
similarity index 100%
rename from protocols/spice/configure.in
rename to protocols/spice/configure.ac
diff --git a/protocols/ssh/configure.in b/protocols/ssh/configure.ac
similarity index 100%
rename from protocols/ssh/configure.in
rename to protocols/ssh/configure.ac
diff --git a/protocols/vnc/Makefile.am b/protocols/vnc/Makefile.am
index 9180cc13..e71b89bf 100644
--- a/protocols/vnc/Makefile.am
+++ b/protocols/vnc/Makefile.am
@@ -37,7 +37,7 @@
 AUTOMAKE_OPTIONS = foreign
 
 ACLOCAL_AMFLAGS = -I m4
-AM_CFLAGS = -Werror -Wall -pedantic -Iinclude
+AM_CFLAGS = -Werror -Wall -pedantic -Iinclude $(LIBGUAC_INCLUDE)
 
 lib_LTLIBRARIES = libguac-client-vnc.la
 
@@ -45,6 +45,7 @@ libguac_client_vnc_la_SOURCES = src/client.c src/vnc_handlers.c src/guac_handler
 noinst_HEADERS = include/client.h include/vnc_handlers.h include/guac_handlers.h include/convert.h
 
 libguac_client_vnc_la_LDFLAGS = -version-info 0:0:0
+libguac_client_vnc_la_LIBADD  = $(LIBGUAC_LTLIB)
 
 EXTRA_DIST = LICENSE
 
diff --git a/protocols/vnc/configure.in b/protocols/vnc/configure.ac
similarity index 74%
rename from protocols/vnc/configure.in
rename to protocols/vnc/configure.ac
index eb3b005c..e9e5e299 100644
--- a/protocols/vnc/configure.in
+++ b/protocols/vnc/configure.ac
@@ -34,24 +34,43 @@
 #
 # ***** END LICENSE BLOCK *****
 
-AC_INIT(src/client.c)
-AM_INIT_AUTOMAKE([libguac-client-vnc], 0.7.2)
-AC_CONFIG_MACRO_DIR([m4])
+AC_PREREQ([2.61])
+AC_INIT([libguac-client-vnc], [0.7.2])
+AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 
-# Checks for programs.
+LT_PREREQ([2.2])
+LT_INIT([dlopen])
+
+AC_CONFIG_MACRO_DIR([m4])
+AC_CONFIG_SRCDIR([src/client.c])
+
+# Programs
 AC_PROG_CC
+AC_PROG_CC_C99
 AC_PROG_LIBTOOL
 
-# Checks for libraries.
-AC_CHECK_LIB([guac], [guac_client_plugin_open],, AC_MSG_ERROR("libguac must be installed first"))
+# Libraries
+AC_CHECK_LIB([pthread], [pthread_create])
 AC_CHECK_LIB([cairo], [cairo_create],, AC_MSG_ERROR("cairo is required for drawing instructions"))
 AC_CHECK_LIB([vncclient], [rfbInitClient],, AC_MSG_ERROR("libvncclient is required"))
 
-# Checks for header files.
-AC_CHECK_HEADERS([stdlib.h string.h syslog.h guacamole/client.h guacamole/socket.h guacamole/protocol.h iconv.h])
+# If bundled copy of libguac found, use that
+if test -d "$srcdir/../../libguac"
+then
+    AC_SUBST([LIBGUAC_LTLIB],   '$(top_builddir)/../../libguac/src/libguac.la')
+    AC_SUBST([LIBGUAC_INCLUDE], '-I$(top_srcdir)/../../libguac/include')
+else
+    AC_CHECK_LIB([guac], [guac_client_plugin_open])
+fi
 
-# Checks for library functions.
+# Functions
 AC_FUNC_MALLOC
+AC_CHECK_FUNCS([memset socket strerror fork])
 
+# Headers
+AC_CHECK_HEADERS([stdlib.h string.h syslog.h iconv.h])
+
+# Done
 AC_CONFIG_FILES([Makefile])
 AC_OUTPUT
+