Assets like these can be created in any 3D package.
They are imported into a game by pre-rendering the models at specified angles, using orthographic projection in the viewport. The pixel effect probably is a side-effect of rendering at a low resolution with little or no anti-aliasing. The spritesheets generated by these will be ordered in such a way that the application can mathematically compute which frames apply to which angles and animation frames.
In Age of Empires 2, you can easily tell that the structures are pre-rendered 3D assets, especially by how they have such a low frame rate of animation. The reason for this is simply disk and memory consumption. Animating large images like those at a high frame rate will bloat the asset sizes tremendously, on disk and in memory. The smaller sprites, e.g. the villagers, can have much higher rates of animation, as they are comparatively small and less intensive. This is also why the units in the game have only 8 directions of rotation, as accommodating all potential rotations and animation frames will, again, bloat disk and memory consumption (not to mention rendering time too).
There are some games however that do use a 3D method for rendering certain objects. Take C&C Tiberian Sun and C&C Red Alert 2 for example. The infantry and structures use pre-rendered sprites, like AOE2. However the vehicles use a 3D rendering technique called "Voxels", which are essentially 3D bitmaps that are rendered in real-time, which is why they have such a large variety of angles and positions, whilst still having that "2.5d" look.
Somewhat Unrelated: Also I believe that 2.5D normally refers to 3D rendered games that use 2D gameplay mechanics. I may be wrong in this case, but that is how I refer to it. :)