The in-game link models are as follows:
alSumou - Farmer Link in Sumo Outfit
Bmdl - Farmer Link
Kmdl - Hero Link (in green tunic)
Mmdl - Magic Armor Link
Wmdl - Wolf Link
ZMdl - Zora Armor Link
In each archive, you will find a set of folders. The models for most are in "bmwr". Inside each "bmwr" folder, you will find usually 5 or 6 files. I'll use the Kmdl, or Hero Link, as an example.
al.bmd - Body
al_bootsh.bmd - Iron Boots (Haven't found out how to properly use these yet)
al_face.bmd - Face
al_hands - the different hand poses
al_head - Hat and Hair
al_swb - The Ordon Sword
All other archives will have a similar naming structure, and some of the models share certain characteristics (namely the face for Hero, Magic, and Farmer and Iron Boots).
The two exceptions are Sumo Link, which the models are stored in the bmdr folder, and all it has is bls.bmd(Body), bls_hands.bmd(handposes), and bls_head.bmd(just the hair). Sumo uses the same face as Farmer, Hero, and Magic Armor Link. The other exception is Wolf Link. Although the models are in the bmwr folder, there are only two files. wl.bmd(wolf link) and wl_kusari.bmd(chain link for shackle).
The face and hat/hair will be at the models feet and up-side down. You need to spin them right-side up and facing front. To do this, I just used the bottom of the hair and the top of the back of the neck (both in the center of the model) to line them up.
As for how to make them pretty, these models were designed for real time rendering, not CGI. I use a program called Blender, merge all double vertices, and set smooth on the model. I also use Sub-Surf, but still need to tweak it to get it to look right.
EDIT: Dark Link is found in Demo18_00 > bmdr. Just look for the model with the name "demo18_dlink_cut00_gp_1/bmd". I haven't found him in-game as of yet, though.