3DS Max is by discreet and Maya is by Alias.

Other modellers:
Wings3D
Milkshape
Blender
Aztec
Metasequoia
ppModeller
gmax
SoftImage

Personally, the power of gmax is hard to beat, plus the price (free), but the export restrictions are a bummer. However, it should be possible to export to MD3 using the freely available tempest plug-in.

Maya Personal Learning Edition (Maya PLE) is a great way to learn Maya, but export is even more limited (almost non-existent). I've heard there is a way to write a script to output the model data to the script output window as text and then you cut and paste it from there.

Blender has a very wierd UI, but after you get used to it, it is apparently quite powerful. I believe {MSX} uses it for his models.

SoftImage have released a free version called XSI for Half-Life 2. It's interface is also quite strange and difficult to get used to.

Milkshape is a simple modeller, but perhaps too simple. The lack of real editing features in the 3D window limit it. Apparently Milkshape 2 is on the way, but it's been on the way for a long time.