For this list, I've defined "Christian fantasy" very broadly. I include books that are clean, family-friendly tales of good versus evil (with Judeo-Christian themes) such as J.R.R. Tolkien's legendary The Lord of The Rings, fiction with more overt Christian imagery like C.S. Lewis' The Chronicles of Narnia, and also explicitly Christian fiction from the likes of Frank Peretti. With that out of the way....
Here are my picks for the must-have Christian fantasy books...
The Lord of the Rings trilogy by J.R.R. Tolkien
The Chronicles of Narnia series by C.S. Lewis
The Screwtape Letters by C.S. Lewis
This Present Darkness and Piercing The Darkness by Frank Peretti
Sorcerer by James Byron Huggins
Nightbringer by James Byron Huggins
The Oath by Frank Peretti
The Door Within by Wayne Thomas Batson
The Descendants Saga by James Somers
There are other Christian fantasy authors I still have to read, such as Stephen Lawhead, Donita K. Paul, Karen Hancock, and Bryan Davis. Their titles may replace some of the above - or be incorporated into some of the above, so check back often.
I haven't yet prepared a list of top Christian science fiction books, but that list will be sure to include:
Leviathan by James Byron Huggins
The Chronicles of Soone by James Somers
God bless you and Happy Reading!