The one that our company uses is internally developed which gives us control of the system. However, it also has limitations and drawbacks and isn't the most user friendly. I don't have any recommendations for you, but definitely would suggest to buy something that is used industry wide since they usually are the most user friendly.
We use Auditor Assistant and developed an issue tracking system in 2007 within Auditor Assistant. When we close an audit database, the audit issues copy over into the issue tracking database. We track over 70 data points for each issue, including management's remediation date; audit testing due date (90 days after mgt remediation); validation testing failures; business unit ownership; primary, secondary and tertiary risk; root cause; legal entity; issued identified by audit or management; and more. Would be happy to discuss over the phone.