My preferred tools for making 3D assets are 3D Studio Max and Photoshop.

3DS is maybe not the most efficient tool anymore for making simple models, but given I have been using it for 12 years I have less of a learning curve (and less time wasted) then with Blender, SoftImage or 3DCoat (all of which I have used and can recommend, even if I'm not proficient at any of them).

For textures I use Photoshop and SSBump Generator for my normal maps.

I rarely do any 2d sprite work, but when I do, I use a scanned hand drawn/colored image and pixelate it in Photoshop.

I use Blender for 3d models, Inkscape for vector artwork, GIMP for 2d raster images, and Genetica 3.5 for seamless textures (The one tool that I use that actually has a license fee).

That being said, my graphics abilities are not very good...

I use MSPaint for 2D, for the most part. If I find myself needing layers, I will do most of the work in Paint and switch to Photoshop later. I hate the Windows 7 version, but I stick with it for its generous number of undo levels (i.e. more than 3).

I've been working with Blender for 3D models for many years now, and I'm trying to wrap my mind around all the layout changes in 2.5.

I also occasionally use MapZone to generate tessellating textures.