I myself don't count season 1, because she didn't kiss him back and in fact shoved away real quick, and it barely got to be a peck of a kiss.
So while it's technically their first kiss, 3x17 is their first real kiss, for sure. Joey doesn't shove away, she doesn't stop it and tell him no, she doesn't seem incredulous that it happened, and kisses him back.
She is surprised it happened, but not baffled like "wow that's out of nowhere" kind of baffled, and she reacts so much more severely than she did in season 1. In season 1 she was actually kind and gentle about it all, because she was in love with Dawson at the time.
Here she's freaking out because she's in love with Pacey too and doesn't want to face it and is scared of what Dawson will say, but she's no longer in love with him, but Pacey.
I mean the differences in her reactions to Pacey kissing her in season 1 vs. season 3 says everything. In season 1, she doesn't want it and loves someone else, so it's NBD to let him down gently.
In season 3, she is so in love with him and has been deluding herself that she doesn't feel that way about him, and now she has to confront how she feels about him and is scared to and reacts wildly in every way she can to deny it is anything real and brings Dawson into it too to remind herself she can't go there.
Also it's different for Pacey as well. In season 1 he was just attracted to her, kinda liked her, but that was it. I'm sure he was bummed she didn't feel that way too, but he got over it quickly and fairly well. In season 3 kissing her is everything for him, and he's so in love with her, and he's scared of her reaction and has to bluster and lie to make it seem like nothing so she won't know he's in love with her, because to him she's rejecting him, but also so he doesn't lose her because she's so important to him.
Ahhh *happy sigh* the progression, I love it
