I’d probably have Jigsaw in my top 10 songs, and can’t immediately think of a bad B-sides from the Fish era. I will give you Emerald Lies as being not one of the best ones though. Each to their own, like you say. When I was watching them live I always thought that Jigsaw would be perfect for H to perform and could be one of those songs from that era that he could ‘own’ (like Warm Wet Circles/TTOTN). Same with Cinderella Search from a similar time too.
I rarely go back to listen to the early H stuff but do still stick the Fish ones on quite a bit. Back in the day Fugazi was my favourite album (probably of all time), but I think the production is probably the weakest on that album and it has aged worst (although it probably still has my favourite two Marillion songs - Incubus and Fugazi). Clutching used to be my least favourite album of that era but I think is probably the one which stands up best with the passing of time (just for the Record aside, of course!).