There is a d20WHFRP Yahoo Group that has done a lot of conversion work already. I haven't read all of it, but one thing that I wasn't super-enthused about was the extent to which they used 3e rules & classes.
I actually have been poking around with some different ideas about ways to do this since an earlier thread on the topic. I too have been considering COC as a better d20 model than D&D for my possible conversion.
One issue I've had, though, is Level-progression. I'm not entirely happy with the way that skills and abilities (Saves, BAB, etc.) all jump each time you level up. I'd prefer a way to have progress as more incremental and individualized (closer to advance schemes in WHFRP, i guess

). One possible way to do this is through having increases in things like Saves and BAB be "purchased" with XP instead of going up in level. This is actually more of a GURPS-like mechanic. You get __XP? You can use that to gain a +1 to your Will Save or Ranged BAB. This may be adding too much complication for too little benefit though.
I do like the templates as opposed to classes. Very easy to make basic careers with templates. Offense v. Defense profile is a nice touch, too. It does make the spellcasters a bit tricky, though. One way I thought of handling wizards, etc. was to make "Levels" in spellcasting (Wizard's Apprentice, etc.) into Feats with certain prerequisites. Like the "Sensitive" Feat in CoC or the "Magery" advantage in GURPS. You'd have to gain the ability to cast minor spells before gaining the ability to cast more & more powerful ones. You'd learn spells one at a time as well, with a limit (probably INT-based) on total spells known. I also have considered using Spellcraft rolls to determine whether a spell is successfully cast or not. Prestige Classes are one option to handle spellcasting, but since the templates aren't exactly classes, that got a bit murky too.
I also thought a score-based Mana Point system would make sense instead of "slots" per day. Perhaps something like INT+WIS. Then, as you gain more spellcasting feats (from Apprentice to Journeyman to Master, etc.) you would gain X amount of mana as you gained more ability.
To reflect the danger of combat, CoCd20 does a pretty good job already. Throw in a few colorful critical hit tables and you're about set. I figured base HP = CON, then flat 1d6 after that (no CON modifier). Massive Damage limit = CON.
Well, that's my half-baked thoery at any rate.