I think twice about it all the time. Not because of the light loss, but the loss of image quality. I know adding the 1.4 Extender will give me more reach and I know I'll have to pay for it when I pull the images up on the computer screen.
It used to be that the bare lens always beat the lens+TC. Now, that statement needs to be revised to, in some cases within the same generation of lenses, the bare lens will always beat the lens + TC. The 600 II + 1.4x III is actually a little sharper
than the 800/5.6, plus it's got a little more reach and is a heck of a lot lighter, for no additional money. So, at the point the only reason to go with an 800/5.6 is if you plan to put a 1.4x on that, which will beat out the 600 II + 2xIII. Likewise, the 500/4 II + 1.4x III is sharper than
the bare 600/4 MkI, and also longer and lighter, perhaps making the 500 II + TC a better choice than the older 600 (more expensive, though). Note that the above assumes the 50% AF speed reduction you get with a 1.4x TC is acceptable (but the superteles focus so fast, 50% slower is still going to be fast).
However, the 400 II + 1.4x is not as sharp
as the bare 500/4 MkI.
So, if comparing the current (MkII) lenses, you're better off getting the focal length you will use most.
Keep in mind that while you can crop, often you cannot back up to get a wider AoV, especially with a long lens where you'd have to back up a lot. Depending on what you shoot, you may want to have a second body with a shorter lens, like a 70-200/2.8 II to pair with a 400/500, or a 100-400 to pair with a 600.
The 200-400/4 + 1.4x if it ever becomes a reality, is worth considering. The zoom is convenient - but of course, only if 560mm f/5.6 is long enough and fast enough. If not, the 500/600 II may be better choices.