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.
For a startup quickbooks is enough. In my last venture the other founder's father was a retired CPA and did our books with quickbooks (gratis!). I would qualify that as an endorsement because if a CPA thinks it is good enough it probably is.
Quickbooks has an online edition. It only works in IE on Windows and is expensive, but it does exist. If there were a good accounting system online, I'd use it (but it'd have to work with Firefox, since I'm on Linux on the desktop).
The problem, of course, is that business accounting is complicated. And you can't easily pick a smaller sub-set of features to launch with (what good is invoicing without a chart of accounts, and what good is a chart of accounts without reconciliation, and you've also gotta be able to import the most popular file formats for bank data imports and such). It would take several people working pretty hard six months to a year to launch the smallest usable feature set, and they'd have to move fast to get to the point where bigger businesses could use it--revenues from very small businesses won't sustain this kind of company.
That's not to say it's not a great business idea. Between shutting down my previous company and starting my current one, I toyed with the idea pretty seriously. I may come back to it in a few years if the need has not yet been met and I'm ready to move on from what I'm doing now.
SugarCRM is kicking ass these days. DFJ invested in it recently. And name recognition is really picking up. We had lots of people asking for us to add support for SugarCRM to our automated script installation module...we finally added it a couple of revisions back...would have added it sooner, if it weren't such a god-awful bear to install. It's really cool, though.
Those of you living The Dream and running a startup and having to do the books: what are you using? Is it enough to just use Quickbooks, or do you have to hire an accountant?
Help out those of us still in the planning stages/stealth mode.
Do both: use QB to keep the books, and have an account check it over quarterly (monthly, yearly, whatever works best for you) to make sure you're not doing anything that will really cost you down the road.
That's what my start-up did.
btw, I would recommend that you don't buy the premier edition: go for the online version. All the bells and whistles can be done by you with other programs, even excel.
I'm also using Quickbooks. It's pretty easy to learn - even if you don't have an accounting background. When I got started I had my tax CPA look over my books to make sure I was doing things right.
Also, you should check out http://oe.quickbooks.com/ - it's an online version of the software, which I've been pretty happy with. Subscription is $20 a month (vs. $150-$400 for the install). It's great for startups that aren't sure how long they're going to be around...
I've been using QB for years. The largest business I know about that uses it is a client of mine, a futures fund LLC managing over 2.5 billion dollars (They use it to manage their business accounts, not the client's money for which they have vast amounts of proprietary software).
You've got to use some kind of program to keep track of number. And it's cheapest to do the books yourself or hire someone to do it part time. Another nice thing about the online edition is it's easier to share your information with your accountant.
I've been tracking both my personal and business finances in ledger for years and couldn't be happier.