This is a question that comes up time and time again, and it depends on what you want out of your system, or out of your business.
Choices are vast, from Sage, Xero, FreeAgent, Quickbooks, Clearbooks, Kashflow, Freshbooks or even just the humble excel file. It is often a personal preference and you could try them all. Some need more set up than others, some you can invite an accountant to monitor what goes one, and some will supposedly hook into the HMRC tax return system (i’ve not tried this).
Ask business colleagues that you trust what they use, how they use it and how they find it. My preferences are Excel, Clearbooks or Xero. For startups, I recommend excel, for people that want something a bit more professional to send invoices and the such, then Clearbooks, but for ability to integrate to other software like a CRM system, bank feeds, scanning systems – then I would recommend Xero in one form or another. We use Xero here at Performance Accountancy. Of course there are times I could have thrown it out the window, and there are things I am still discovering, but it is work the upfront effort somebody needs to put in.