We use many different systems depending on what suits the clients needs best. For most micro businesses we have Excel spreadsheets that we get them to complete. If there requirements are above this then we get them on to something like Iris Openbooks (click on the link to read my blog on why) which is our preferred choice.
If the client is already using something else then we will accommodate that also as most software is pretty comparable these days and I think we should be flexible and allow clients to use what suits them and their business. The days of forcing someone to use Sage are long gone.