Choose what size case you want and go from there. ITX, mATX, or ATX. ITX is tiny, mATX is medium and ATX is large. There are other sizes too, like EATX, but those are much more feature rich boards, usually, necessitating the larger size, and you won't need one of those.

So, if you chose an ITX case, like a Corsair 250D, we would suggest an ITX motherboard and GPU that would fit the case.

If you chose an ATX case, like a corsair 300R, we'd suggest an ATX board.

The main advantages of going bigger are room to work with the case (easier to build in) and also expandability. In an ITX case you can fit 1 GPU. an mATX case/mobo can typically fit 2, and an ATX mobo/case can fit 3 or 4. Doesn't just have to be GPUs, there are PCIE SSDs, sound cards, wifi cards, etc etc. Also, larger boards tend to pack in more features. The ASRock Z97 Extreme 6, an ATX board, has 2 M.2 slots on it. You couldn't fit that onto an ITX board. You'll also usually get more SATA ports on a larger board. Also, ITX boards only have 2 RAM slots, while larger boards have 4. (on s2011 they have up to 8 but you aren't looking at that socket)

Here are an ITX, mATX and ATX boards all together showing size difference.