I also use Moneysoft Payroll - the Payroll costs me £120 per year for unlimited clients and comes with a FREE module to CIS which is very good. You can file the reports online through the software, and it creates very professional looking Deduction Statements for the Sub-Contractors.
I am not responsbile for the Payroll for the client I use it for, yet I was still able to set up the CIS part of the module. It even allows you to email the statements directly to the Sub-contractors individually or as a group to the Client for them to send out directly.
I have no experience of any other software, and previously used the FREE HMRC online filing system and Excel.