My favorite movie of The Secret Garden is the 1987 Hallmark Hall of Fame version. It's probably the one that changes the most from the book- Colin and Mary are not related in this version and it also includes a grown up Mary coming back to Misselthwaite Manor. The reason this is my favorite, though, is probably because it was my first introduction to The Secret Garden. Up until that point, I stuck solely to The Baby Sitters Club books was wasn't interested in reading anything else.
Next up is the 1949 version. One of the biggest travesties is that this movie is not available on DVD. Luckily, I do have a VHS copy and, for this and one other movie not on DVD, I've held onto a VCR that works.
Then would be the Warner Brothers 1993 version. This version created a little more mystery than the other versions and had the best sets. I also really liked Mary in this version.
An honorable mention is The Secret Garden musical. I saw it years ago when it was in Birmingham and I loved it.