Three recent papers that contradict Lott's "More Guns, Less Crime" theory:
Duwe, Kovandzic and Moody, "The Impact of Right-to-Carry Concealed Firearm Laws on Mass Public Shootings" Homicide Studies Journal, 6:4 pp 271-296 (2002). Duwe et al find no statistically significant impact of carry laws on mass public shootings, contradicting Lott's claims in his new book and an earlier paper with Landes. (Lott does not even mention this paper in his book.) Even when they tried to replicate Lott's results they could not find a significant effect.
Helland and Tabarrok in Using Placebo Laws to Test "More Guns, Less Crime" : A Note tested the theory by comparing Lott's results with regressions run where instead of the actual carry laws being used, placebo laws were assigned to random states. This gives a better idea on whether Lott's results could have arisen by chance than the standard tests. Carry laws were found not to have had a statistically significant on crime rates. The only thing that could not be explained by chance is the combination of a decrease in violent crime and an increase in property crime, but as Ayres and Donohue point out, the decrease in robbery is far too small to explain (by substitution) even a small part of the increase in property crime.
Kovandzic and Marvell in Right-to-carry Concealed Handguns and Violent Crime: Crime Control Through Gun Decontrol? looked at how the number of concealed-carry permits in each county in Florida related to changes in crime. No significant effects were found and there were about an equal number of increases and decreases.