Arjen's stuff is hit/miss for me. I like some of Ayreon's stuff, but I love Star One, especially the live CD/DVD. Dream Theater is one of my fav bands, so I've got most of the side project stuff, which is again hit or miss. I just saw Liquid Tension Experiment (Portnoy/Petrucci/Rudess/Levin) live at NEARfest which was incredible. I've only gotten in Mastodon within the last year or two, but I freakin' love 'em. While Blood Moutain is great, Leviathan is a monster!
I'm kinda in the same boat. I'm not religous at all and tend towards the athiest side. I dig a lot of classic prog like Yes, ELP, King Crimson etc ... Spock's Beard has been one of my fav prog groups for years. A few years back, thier frontman became a born-again, and left the Beard to do solo Christian prog stuff. We're talking heavy Christian vibe, but the music is still some of his best stuff. It dsoesn't bother me in any way at all. Good music is good music!