What is the general consensus with regards to filling in any channels that were cut for wire, plumbing, etc?  Proportionally, it isn't much compared to the whole wall, and on my home, the exterior foam is very solid with almost no channels or cutouts where there is concrete.  Of course, there are penetrations and whatnot, but not just foam removed.

Is the heat loss pretty minimal? 

It would be pretty time consuming and expensive to use tube foam to fill in everything.  My builder is foam filling the channels with pipes so that they don't rattle, but the ones with wires, i think he will leave as an empty channel.  He is using foam pieces to keep the wire close to the concrete versus letting it float around the channel.

Fill channels with low-e foam. Insulation loss is minimal, but you want to maintain a continuous vapour barrier. Also, this will keep the wires well below the surface to minimize chances of hitting the wires with drywall screws, etc.

Fill it in. You don't need bug runways in there.

Get a foam gun that uses 24 oz. cans. They are much better, and cheaper in the long run rather than the homeowner stuff. If you leave the can on the gun, it will go months without going bad. You need to pay attention to where those channels are going. On one floor, going horizontally, they shouldn't make a measurable difference. But going into the attic or basement/crawl, you have created a conduit for air leakage. I've been crawling all over my attic prepping for insulation, sealing all of the various penetrations. I'll do the same in the basement.

I plan to see what it looks like after they put in the attic insulation.  They should start early next week.  They actually foamed in the wires, now, so there is less and less space that needs to be filled.  I will probably just leave it as it is now, but I will go and check it out later to see how much foam they are using to hold in all of the wires.