from looking at some of the citations, number 6 and 7 in particular, it appears as if you really need to take into consideration how they're counting.
the 1.5 percent figure comes from lining up similar sequences and counting the number of base substitutions but not the segments in between.
as the chimpanzee consortium noted,
the figure reflects only base substitutions,
not the many stretches of DNA that have
been inserted or deleted in the genomes.
The chimp consortium calculated that these
“indels,” which can disrupt genes and
cause serious diseases such as cystic fibrosis,
alone accounted for about a 3% additional
difference (Science, 2 September
2005, p. 1468)." - the 6th citation in the wikipedia article.
subsequent research has apparently shown that there's also significant differences in the number of copies.
on top of all this, you've got to take into consideration that there's really only one system we're interested in, the brain... where that same link says that computational studies... bleh for lack of a better way, they inferred that genetic coexpression was correlated to functional relevance, in other words that the more tightly 2 genes were found to be on or off together, the more likely that they both would have some important role in the tissue, otherwise there'd be no real point to linking them. Apparently when they compared cortex tissue between the species, 17 percent of the this genetic linkage was exclusive to the human cortex.
Regardless of the numbers/conclusions, it does bring up a number of concerns when saying we're 98 percent similar genetically to chimps.
are you counting by:
differences found in similar sequences?
are you taking into account gene positions?
number of copies of the genes?
distribution of the differences?
what happens if 95% of our genes are keeping us alive/keeping the species going, and the rest goes into that lb of gray matter between our ears? how much of that 1 % is in that 5%?