Should I keep my Canon 400D or Sony NEX-5 when upgrading to a Canon 550D/600D?

Just from personal experience, I suggest grabbing either the 550D or 60D and selling the Sony. (If I had my preference, I'd keep the Sony too, though.) Reasons:

• Same lenses, similar capabilities (no manual focus)
• Use existing workflow
• Use existing knowledge of how Canon cameras work (important, IMNSHO. It is critical that you can use your camera without having to always look for the buttons!)
• Good backup to your new Canon.

Personally, I have two Canon bodies (450D and 500D) with some sweet glass on them, and then my Olympus E-P1 for more casual/vacation shooting. I love both systems, and both can produce fine images, but the glass available for Canon (or other dSLRs) is fantastic, and I won't part with it, especially since I already have it. ;-)

I've done enough manual focus work to know that in fast situations that it, to me anyway, would be annoying. I'd rather have AF than none at all, especially since my eyes will frequently lie to me if something is or isn't in focus (Contacts + astigmatism. Diopter adj helps, but not completely).

If you can, keep them all; but if keeping the same lenses (with the same capabilities) and the same workflow is important, then get another Canon and sell the Sony.

(Side point: Note that your adapter is going to require the use of your Canon-mount lenses wide-open. Which means your 50mm is always at 1.4, and your 28 is always at 1.8. Not the sharpest point of either lens, and likely not always what you're after in terms of DoF. Some lenses will let you stop down manually -- perhaps the Sigma does -- don't know though. Canon lenses rarely do, however, so that is also a point to think about.)