I have hundreds of Phish recordings and like different ones for different reasons. I tend to like the audience recordings best because they sound more like the concerts did than anything. I find that the soundboard recordings sound very little like the shows did. They don't give me the feeling that I got when I used to see them live. Most people wouldn't consider the audience recordings close to the quality of the soundboard recordings because they don't have most of those audiophile characteristics, but they sure transport you to the show! Then there's those "matrix" recordings that are a mix of a soundboard and audience recording which can sometimes be quite satisfying... The shows were what that band was all about and that's what I want to hear when I listen to them now.
Now, if we're talking about bands that I havn't seen live, I tend to like the soundboard recordings more. I'm assume that this is because I just don't know what they sounded like live and prefer the added detail and instrument separation of the soundboards.
If you have seen lots of Phish you may be content with good quality audience recordings. If not, the soundboards might do it for you! As for which ones to seek out, I don't know. I rank them in my head for content only but there are many that are great shows that also sound really good.
A great reference is http://db.etree.org/shnlist.php?artist=4&year=2004
This is the largest database of the known "circulating" Phish recordings. Most shows have multiple recordings listed, many with comments. It's easy to find a good recording of a particular show using the database.
What a band. They were a rare 4 who made magic consistently from night to night. They are missed very much.