Shorter speaker runs or shorter IC Runs...Which is the better set up and why?

If the components adhere to the balanced design, then using long XLR's have no effect upon sound quality.
Keeping the speaker cables short, say under 6-8 feet, would be the best way to keep costs down, and minimize effects from the cable itself.
B

I don't have a real preference as to the length of either, but more towards the connection being made at each end. Interestingly, Maple Shade strongly recommends the opposite, i.e. long speaker cable (no less than 8'), and short interconnects. I would think that both should be as short as possible, but not too short! Heh, heh, you ought to see me try and make something reach when there is a safer choice at hand. 
 When I think about it though, the interconnects are trying to send a 1-2 volt signal on to the next in line, whereas the speaker cables don't have that same issue coming right out of a power amp.

When I went to long XLR connections and short speaker cable runs decades ago the improvement in clarity was immediately obvious! Better bass impact too- the improvement was across the board.

If your gear supports the balanced standard (AES48) then the length and cost of the interconnects is almost immaterial. OTOH speaker cables have a big effect and the shorter you can make them the better.

Longer speaker wire (unless talking >50ft) only effect wattage loss and lower damping factor, which can be negated by using a thicker gauge.

Longer interconnects do have worse crosstalk and jitter (if talking digital), but a good DAC should take care of the latter and crosstalk has to be immensely bad (above -40dBFS) to be noticeable, which I don’t even think a 50ft RCA would have audibly poor crosstalk; but frequency response, THD, IMD, etc. are almost always near identical to a short interconnect.

@mzk,
The OP stated he is using XLR cables. Length will have no impact on sound.

Longer speaker wire (unless talking >50ft) only effect wattage loss and lower damping factor, which can be negated by using a thicker gauge.

I disagree totally. How the cable is designed, what materials, etc. contribute to how they will reproduce sound.
B