I have just started using this:
http://www.freeagentcentral.com/index
I like it because it seems to take care of everything concerned with running a small contractor/freelance business (including paye and dividends) and most importantly keeps me 100% informed of the financial and tax position of my Ltd Co and my Self Assessment in real time (also I hate complex spreadsheets which this does away with). Also great support and a growing user base following.
Many accountants support it. You can export a ledger from it and email it to your accountant or even give them a login for it to keep them up to date with your accounts. Some accountants include the subscription fee in their price. It's £25 per month to subscribe to for a Ltd co. [I can provide a link for 10% discount privately if PM'd but won't quote that here due to forum rules].