At the moment these are my favourite fanfics:
Favourite Harry Potter fanfic: On the Way to Greatness (Mira Mirth)
Other writers that definitely need to be mentioned as being awesome include
The best collection of good Harry Potter fanfiction is definitely the DLP C2 (See Communities)
If you've gone through that C2, go and check out DLP itself (Or do it first). Great forum for Harry Potter and Dresden Files discussion and stories.