When I think about it, I didn't really like the Final Weapon theme. I liked the Space Port theme for what it was, definitely fit the situation, but Final Weapon? It's ok the first few minutes, then it just gets repetitive and easily stuck in your head, but not in the good way.
X5's boss theme, I like it, It's a good listen, it's just a strange boss theme to me though. Not a bad one, just... strange. Definitely unique. Id have to agree on Zero's intro theme in X5 being forgettable. It's good, but just cant hold up to X4's Zero theme. (which set the bar pretty high as far as Zero themes go, and Post X4 has really only the Command Mission's Zero theme to call competition, despite it being more of a slower paced theme like X5's.)
possibly two of my favorute X4 themes are, aside from the obvious X/Zero themes and Jet Stingray, have to be the Double theme and Both Sigma themes. Particularly the second, though the first one is definitely pretty unique IMO.
And the Dr. Light Capsule is still my favorite in the X series, although the X8 one comes close, held back only by the fact that they use a differently instrumented version for the R&D lab.