Good question. As a fan, I'ld have to say "Just buy them all!", but that's not how it goes. My favourites:
The Answer Machine? - Probably their most melodic and melancholic album.
Jonah's Ark - Their breakthrough album, contains "Thinking allowed?" which is probably their most accessible song. All in all one of their lighter albums.
Irrational Anthems - Probably their biggest seller. Maybe the album that best sums up what Skyclad is, so maybe you start with this one.
The Silent Whales of Lunar Sea - This a bit more experimental, more keyboards than on other albums, more complex rhythms, more artsy.