I had been contemplating both as well. The 100L has the advantage of being a good portrait lens AND a very good macro lens. However, I decided to go with the 135L. Why? Because it's a focal length that I'm more accustomed to for portraits and since portraits were the main objective I decided to go with the hammer-over-swiss-army-knife approach. If the main goal had been macros I would have looked at it the other way.
Both are excellent lenses and (don't tell Canon that) really good value - if not a bargain compared to how much other very very good lenses cost.
For me personally, the IS in the 100L counts as a negative so that was another (small) factor.
I'm quite happy with the 135 and it performs really well. It's so sharp that at times you might want to carefully evaluate in post processing if you really want it that sharp depending on the subject...The bokeh is probably as good as it gets.
That being said: I may add the 100L at some point as well - as a macro lens. But since I'm not very interested in macro work at the moment it's somewhat lower on my list. And even then I may actually go with the TS-E 90 to cover that...
Would you mind explaining why IS on the 100 counts as a negative?
More stuff that you pay for, more stuff that breaks eventually and I personally see absolutely no use for IS other than increasing the keeper rate on borderline useful snapshots in low light perhaps. It's not a replacement for a tripod in situations where you'd want one. And it doesn't help when things are moving around.
Got it. Then I'm a bit confused as to why you were comparing the 135 to the 100 L rather than the significantly cheaper, but still optically exceptional 100 macro. For me, the excellent hybrid IS and weather sealing of the L are worth the difference...