Make sure that the motherboard you get has support for the processor that you will get. For intel processors, you should get an intel P3x or a G3x based motherboard. For an AMD processor, you should get an AMD 7xx based motherboard or an nVidia 7xxa motherboard. These refer to the motherboard controller chips (commonly refered to as the northbridge). They do not refer to the motherboard manufacturers.
At the moment there are two types of memory on the market: DDR2 and DDR3. DDR3 is newer, faster, and much more expensive. You should get DDR2; it is cheaper and almost as fast. Most motherboards support one or the other, but some support both. You could get a motherboard that supports both DDR2 and DDR3 if you plan on upgrading later, but otherwise, a DDR2 motherboard would be better and cheaper.
Most higher-end motherboard features are intended for over-clockers, such as large motherboard heatsinks, advanced power systems, ect. If you are not overclocking you will not need them.
Nonetheless, there are some other features you should consider.
RAID (Redundant array of independant disks) is a method of connecting multiple drives together to appear as one disks. There are multiple variations on this, each with their own advantages. The two most basic and most common types are RAID0 and RAID1. In RAID0, two or more disks are combined so that (for example) two 500GB drives appear as one 1000GB drive. This can increase overall disk bandwidth. In RAID1, the disks are combined so that all data is written to both disks. The disks are copies of each other. The advantage here is that if one disk fails, you have a perfect copy so you don't lose any data. There are several other variations, look online for more information.
Since you will be doing 3D work, you will not want integrated graphics (the one built in to the motherboard). This does not mean you cannot get a motherboard with integrated graphics, but you will not be using it. You need to make sure the motherboard has a PCI-Express x16 slot.
Beyond that, just look for a motherboard that has expansion slots (PCI slots, PCI-Express slots) in the configuration that you need them.