Lunar Strain is very amateur sounding. I mean, it's great for what it was and it was definitely revolutionary soundwise for its time, but it seems like several of the songs were cobbled together too quickly. You can understand this when Jesper said in an interview that they had to quickly write songs for it, since they only had (initally) three when they heard they got signed to Wrong Again (after having lied to the label about having more songs, lol!) Several songs came out wonderfully -- the ones on the original IF demo ruled of course, and "Behind Space" is obviously a classic. "Dreamscape" seems a bit boring, although it's kind of a catchy repetitive riff. "Lunar Strain" sounds like a bunch of disparate riffs smashed together -- it sounds a bit forced and wobbly, although it had its moments. "Starforsaken" is all right, average I guess. "Everlost, Pt.1" puts me to sleep (In Flames should never do doom metal!), although part two is pretty. Oh yeah, and the drumming on this album is clumsy...
IMHO, Subterranean is where they found their footing. Basically all the tracks sound awesome and sound like classic IF (Lunar Strain sounded like they were searching for a sound, trying all sorts of things), although "Biosphere" is a bit off, but I think it's the recording quality more than anything. And, then of course, Anders came, TJR was released, and there was much rejoicing. The rest is history.
Personally, it's hard to decide on their best album. Right now I'm really digging the new one, actually. Clayman would be my all time favorite, I think. Powerful production, great songs, fucking ballsy riffs all over. The culmination of the classic period of In Flames, before the sudden experimentation (although you can hear the beginnings of weird experiments on Clayman).