How can I improve this Makefile?
Yes:

CXX       = g++
#
# Notice the +=.  Use CPPFLAGS rather than INC for pre-processor rules.
#
CPPFLAGS += -Iinclude/ -I../tools/
CXXFLAGS += -std=c++0x

#
# Move the backslash
# This will stop it looking like a directory at first glance.
binaries=01sum35              \
     02evenfibs               \
     03largestprimefactor     \
     04largestpallyproduct    \
     05smallestmultiple       \
     06sumsquaredifference    \
     07tenthousandfirstprime  \
     08largestproductinseries \
     09specialpythagtriplet

all: $(binaries)

clean:
    rm -f $(binaries)

# Default rules and dependencies works for all the targets
# except the following which need one more file (dependency)

04largestpallyproduct:      04largestpallyproduct.cc    ../tools/tools.cc
07tenthousandfirstprime:    07tenthousandfirstprime.cc  ../tools/tools.cc
08largestproductinseries:   08largestproductinseries.cc ../tools/tools.cc