What is the 'best' will invoke many different responses.
Go out and find a PC magazine which has a comparision of performance of
Mobos or even complete systems. These could include PCs from HP, Dell or
whatever.
The tests should include application performance.
Now, when you find a PC that works 'best' for the type of work do do, then
look to see which company made the Mobo.
Otherwise, if you have a hard on for a CPU; then go to see which Mobos are
certified by the CPU manufacturer.
Keep in mind; many Mobos made today can include all these 'on-board' extras:
NIC
AGP
Audio
USB
SATA
You may want a 'performance' video card, so make sure that the Mobo you
choose, does not have the on-board device. Or you may not want to go to
Serial-ATA Hard Disk, so again, why buy something you don't need.
Do some research, find out the CPU you want, the video you want, the disk
types, etc. Now you're starting to determine the specification for your Mobo
and can 'select' from all the different items made.