For a long time, accounting was one of the few missing Linux functions. Not anymore. There are now some top notch accounting solutions, especially for experienced bookkeepers.
We use and host the fantastic LedgerSMB program. This software provides double-entry accounting, includes a Point-Of-Sale module, Accounts Receivable, Accounts Payable, customizable invoices and receipts, and many other features you need in an accounting package. The main things missing are payroll and integration with other business systems.
LedgerSMB is a true multi-user, multi-location system. It runs on a web server, and can be accessed from any network-connected device, including many PDAs.
We can provide the integration with other systems, custom reports for your business, and other needs.
We also work with GnuCash on a daily basis. This is a desktop Linux accounting application that has some nice reports, online banking, and several other great features.
Not only can we help you with the software, we have several CPA partners who can help get your books set up right the first time to fit your business reporting needs. We can include their services as part of our service contract, for the purposes of setting up your accounting systems properly.