Timber! makes all the logs in a tree break when you hit the bottom block of the tree with an axe of any type. You can toggle this effect to safely remove logs by holding down C while chopping logs with your axe (configurable in /.minecraft/config/mod_Timber.cfg).
Axes added by other mods will not work by default, you will have to edit the Timber! config file (see above) and add the ids for the mod axes manually. The ids for the vanilla axes and the PlasticCraft axe is included by default.