Gatherbuddy(2) does things like mining, herbing, and skinning. Basically, it gathers. It's a gathering botbase. Honorbuddy does things like questing, grinding, dungeons, profession leveling (via professionbuddy botbase, contained in Honorbuddy), and also has botbases that are meant to control only combat while the player handles all movement (LazyRaider / Raidbot / Combat bot), and it can also do battlegrounds and arenas.
So, I guess, in a nutshell Gatherbuddy handles your gathering needs while Honorbuddy does practically everything else.