One thing our business does that every other business does is vacation and overtime tracking. We have a custom in house application for that and we've yet to find a commercial replacement that is, in anyway, half decent. For most Payroll/HR systems, this is merely an add-on feature and doesn't get much attention.
For overtime, integration with our financial system allows overtime to be charged to the correct files and this is something that nobody does (or does well). Probably doing just this little bit makes this project pay for itself.