Currently, we use an Access db to track CAPA activities, generate forms, reports, and queries for specific analysis. As far as prompts and notifications, weekly reporting uses on screen prompts helps the administrator to quickly assess what's currently going on while the reporting uses conditional formats to highlight areas needing attention. The nice thing about using Access is the availability of snapshot files which can be sent to most anyone (as long as you have a Microsoft platform). Even if a person doesn't have Acces as an installed application, they can open the reports through the Snapshot viewer. It's pretty slick.
As a means of reminders, I use Microsoft Outlook in conjunction with Access. I enter due dates to prompt myself of required activities. You may want to give this a shot. Otherwise, there's a host of software out there you can buy, but personally, it hasn't worked very well with CAPA systems I've designed. I found myself throwing it out and building our own system. Word and Excel are equally effective in getting the job done as Dave points out. Keep it simple.
Regards,
Kevin