I haven't played all of them, but my favorite is between 6 and 10.

FFX was the best for me, I loved every aspect of it.
FF9 was also pretty good with very likable characters.

I have played and beaten all of FF games from FF1-FF13 here is my list.

1.VII

2.IX

3.VI

4.X

5.VIII

6.V

7.IV

8.XII

9. III

10.I

11.II

12.XIII 

Left out XI as it was an online game and FFXV as I have yet to play it.

X was a fantastic game and the last real Final Fantasy. I was bummed that they did away with the world map but I felt that they got Tidus and Yuna's love story Right. I find their story much more convincing and superior to that of Squall and Rinoa in VIII.

Easily 9

IX without question. It's my favourite game ever in general. The rest of the games are a bit more difficult to put in order. Of the main series I've played every single game through except II, XI and XIV including the sequels to X and XIII, as well as most of the games related VII. I've also played a lot of the spin-offs, like Dissidia and Type-0.1.

I guess my top 5 would go something like this:
1. IX
2. VI
3. X
4. VIII
5. VII
Though besides IX, the rest of them could be in almost any order, depending on the day.

Here's my top 5:

1. Final Fantasy IX
2. Final Fantasy VII
3. Final Fantasy XV
4. Final Fantasy VIII
5. Final Fantasy VI

FFVI is by far my favorite out of the ones I've played

Top 3 are easy to pick. Bottom 3 are even easier to pick (barfs). The rest could shuffle up and down a little depending on my mood and how strong the nostalgia is that day. My first ever NES game was Final Fantasy, so I got in on the ground floor with this one.

6
7
4
12
9
1
5
15
3
2
8
10
13

FF7 is my favourite, dreading the remake.

But it's like a little bit, FF9, 8, 6 and 12... man... love them all. FF isn't the same games anymore. I want the ATB tactical gameplay back.