I can't recommend ledger, http://newartisans.com/ledger.html highly enough. It is definitely a hacker class tool: command line based with tons of options, transactions stored in simple text files, and very flexible. That said it provides full double-entry accounting and every report you could want including output suitable for gnuplot. Oh and of course it's free and open source.

I've been tracking both my personal and business finances in ledger for years and couldn't be happier.