There are quite a few differences, starting from pump position (in CPU block vs on tube vs in / on radiator), overall design (Asetek vs. other white-label manufacturers vs. in-house designs), flexibility of the tubes, tube length, inlet / outlet port positions, refill port positions (that may or may not clash with other components, see eg. my S396 mod build), and yeah, fans, too. Yes, there are better fans than the classic Noctuas, even noise-wise (and depending on your individual hearing, you might prefer the sound of a particular high-performance fan over Noctua).
I'd suggest watching a few videos on YouTube about this topic, eg. the following one by Hardware Canucks (its why I helped myself to the Thermalright Frozen Edge, which is now gonna save my sorry ass 
)
[MEDIA=youtube]8ntIhvtzgUg[/MEDIA]
Edit: Obviously, Arctic LF II / III is EXCLUDED, as it WONT fit, except if you added a top extension; 38 mm + 25 mm = 63 mm, but max size for anything inside the top compartment is, AT best, 59 mm. Official support is 55 mm height at max.
Also, a bit more infodumping: Thats really the max space. The case is actually just 135ish mm wide, and the side panels add the rest of the 4 - 5ish mm. I've researched, measured and calipered a lot since end of May this year
cu, w0lf.
