I use Ultra Recall every day. Everything (web clips, attachments, links, etc.) is in a single file and it is very reliable. MyInfo also meets your criteria and is similar but simpler in my opinion. TheBrain and Scrivener are interesting options too, but the data is kept in multiple files. If you are looking to add scheduling, tasks and notes, there is EssentialPIM. It stores everything in one file. For complex outlines nothing beats InfoQube. Like Ultra Recall, I rely on IQ every day.

Jon