Personally I've always kind of considered Valis III and IV as the elite games in the series.  Valis III has moments in it that really felt like I was in the middle of a truly unique gaming experience.  With the cut scenes between levels, diving off a roof top to grab a sword and fly back up to kick some ass (in my pajamas!!)  WITH PARALLAX!!  I love the soundtrack of Valis III and actually would consider it a decent opponent to the Castlevania series for recommendations to those that are looking for a good platformer/action game to try out once you've played all the great Castlevania games to death.
When I first played Valis IV it was on the SNES and I actually really enjoyed it!  I loved the soundtrack (again, and I know it's no PCE, but it's still memorable) and thought the gameplay was pretty fluid.  Fastforward to when I finally got it on CD and I was totally blown away at the soundtrack and cut scenes.  It was like a Special/Complete Edition of the SNES version I tried.
I can't say I've ever played Valis I's remake on Super CD, but after reading this thread I might have to seek it out.  I've dabbled with Valis II on Turbo and for some reason or another I was just incredibly underwhelmed by it.  The music seemed fine, but the graphics and controls just felt... 
off to me.  I will have to give it another try some time.  

I've also played "Syd of Valis" on Genesis and it never really caught on with me either.  I understand this was a cute remix of Valis II also, so I dunno.  
All around, I loved 3 and 4, but didn't have that memorable moment with 2.  My experience with the original or the SCD remake is extremely limited.  I will have to fix that.
at the end of 2014 my order of favorites would go like this-
Valis III - Valis IV - Valis 2 - (Undecided Valis I)