Wild Arms is one of the few series I've actually managed to follow, and by follow I mean have enough interest in it to buy a game in the series when I have the money.
The first one brings back memories. I still think it's the best one, since its story and length were both more than acceptable. It also has a nice soundtrack. The Alter Code: F version was alright, but it somehow didn't seem as good. On the plus side I was able to use Jane Maxwell and Zed as playable characters, so I guess that's something. For some reason there's always been a special place in my heart for Zed. ;p
The second one didn't really interest me. By now, as I look back, I can only really remember Marivel Armitage fondly. She was a secret character with no real affect on the main plot, but I found her charming regardless. I guess it was the whole Crimson Noble thing. ;/
The third is my favorite. I'd probably say that it is also the best one if not for the likelihood of the first laying at least some of the ground work for it. It's been a while, so I'd have to play it again to see if I remember if that's correct. Anyway, I just loved the cel-shaded characters, I thought the characters were all highly customizable to ones wants and needs, and the soundtrack wasn't too bad, either. The story was also nice, and when you thought it was all over... Oh, noes! XD
I'm still trying to forget the fourth one. I dunno... It just rubbed me the wrong way. The story didn't interest me, and this whole thing about kids and adults seemed retarded. The new battlefield tactics was a decent change from standard, I guess, but the characters weren't as customizable as before, which, to me, is among the biggest drags in any game.
The fifth seemed to pick up the same attitude as the fourth, and also had a childish air to it that made me gag. The story, as far as I got, was meh. (The extra stuff before the final boss got too tedious, so I dropped the game.) I think it's better than the fourth, but I'm not exactly sure why. Must be because of Rebecca and Avril; two cute girls that are actually good in battle. ;/
So, yeah... It's the first and third, for me. Okay, your turn. Or something like that.