[geoelectric]

I'll join in with recommending YNAB, with a caveat that it's really an opinionated methodology encoded into software, and the main benefit IMO is from the methodology. A comparison might be OmniFocus vs. GTD.

I haven't used the newer web-based version enough yet to know whether you can really roll your own system on top of it, but I suspect you'll find path of least resistance is to do it their way. The good news there is that they explain their way very well, with lots of supplementary material available.