FragMOTION is a new promising tool focusing on bringing professional animation tools to people with little cash.
I worked with the creator to make it fully support HL2 .smd so obviously i had to mention it here :)

You can download a trial from Fragmosoft.com

Exporting from FragMOTOIN is straight forwarded and hard to screw up. Basically any geometry you make will export properly, but to make something with more then one color you will need to make a UV and assign some materials.
To do this go to Texture->Unwrap UV Coordinates and selecting the a more or less flat part of your geometry with the Select face tool in the select category.
then press Project in the unwrap dialog. you will able to edit the projection by selecting a tool vi the radio buttons in the unwrap dialog. when you are done unwrapping press Assign UV and then Done, if you want to change the UV later you will have to that from the Map UV Coordinates dialog, also found in the Texture menu there you can also see the texture as background.

Next you will create and assign a material.
Go to the Textures tab, Right click and select new->texture to add a new texture. Now right click on the empty texture and select open texture to load a texture in to it. Next go to the Model and right click on the Materials leaf create a new material, then drag you texture from the texture leaf on to your material.

To assign the material use the Select face tool to select you geometry and then go in to the Texture menu and pick Assign material. then you just have to select your matial form the list and hit Ok.

Finally exporting. File->export pick the Half-life 2 SMD as the save type, give it a name press Save then select Mesh and press Ok and your done.