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I've fixed my tunnels, but it was a big pain in the butt... here's what I WAS doing when it looked like crap:
I created a prefab of sorts (just copy/pasted really) for each section of the tunnels. So I had a "prefab" for a long straight sections, a "prefab" for a 90 degree turn, a "prefab" for the large areas where the big pipes are, etc... I then pieced these together over the length of tunnel to get the whole thing to have the curved top. So, as you saw, that made some funky looking light maps since the faces of all of the tunnel walls did not meet up evenly.
Here's what I did to FIX it: Created a SINGLE "prefab" for a straight section and placed it in the tunnel. I then cloned one and rotated it 90 degrees and place the rest. Then I used the clip tool wherever they met at a 90 degree angle to get them to blend into one another without overlapping.
In addition to this, rather than having these curved pieces line up with the existing square tunnel, I made sure that they extended all the way to the floor. The only reason I have the basic square tunnel that I'm slapping these curved arch peices into is because the curved peieces are all func_detail so they don't seal the level.
Last but not least, previously the two peices that met at the peak of the arch didn't have any thickness to them... what I mean is, the ceiling from the basic square tunnel was immediately above the point at which they connected and this caused a strange ripping effect at the top of the tunnel. So to fix that, I gave myself an extra verticy and made the top peices one unit thick so that the ceiling didn't rip/bleed through. Here's a screenshot of the before and after (obviously the after is also smoother, but that had nothing to do with fixing the strange lightmaps):

Anyway I don't know if that all makes sense to anyone but basically it was due to the faces not lining up properly.