Jimmy and his vessel died at the end of S4 when he stood with Chuck against the not-identified archangel. Castiel's reconstitution in a shape replicating his former vessel was an act of whomever yanked the Winchesters out of the abbey and put them on a plane. It was assumed at the time to be God. And at the time, we were told that Jimmy was no more. However,

My Bloody Valentine mussed things up with the vessel cravings

So I don't know if Jimmy is actually still in there to take repossession or not.

Anna reconstituted a container in the shape of her former vessel because she liked it and it was familiar. In her case the original owner of the orignial vessel was actually Anna, void of grace.

Lucifer has not stated that Sam would be ruined. He has rather pointedly avoided saying anything about the condition of Sam's personality, identity, or soul, post-claiming. It's my presumption that his arrogance holds everything but Sam's physical ability to contain his Luciferness in abject contempt, and he wouldn't even consider giving it a second thought. Sam must agree to accept Lucifer so Luci can claim his vessel, then Sam is done. The implication being that Sam's soul is burnt up and the atoms scattered, along with everything that makes him Sam.

In The End, the writers were very careful to not have Luci say, "He's in here with me, you brother." There was no Sam, Sam was gone. And that, I think, is a choice made by Lucifer.

Michael made the choice to promise. Whether he honors that promise, or whether the promise is good to anyone but Dean remains to be seen.

Castiel's reconstitution in a shape replicating his former vessel was an act of whomever yanked the Winchesters out of the abbey and put them on a plane

Didn't we learn that God did this, in the Garden/Heaven ep?

And I'm going with Castiel having a speck of mojo left.

I think he still has some kind of mojo left. Otherwise how would he have known about Michael having decided to use Adam as his vessel? Would Cas still be picking up Angel Radio signals if he had no mojo left?

an act of whomever yanked the Winchesters out of the abbey and put them on a plane

I thought in "Dark Side of the Moon" that Joshua told the guys that God did that.

Probably. I don't remember it being actually stated in so many words, but Joshua may have said it and my retention is poor. Of course God can stuff Jimmy back in the box, no prob.

the not-identified archangel

They identified him. It was Raphael ("You were wasted by a teenage mutant ninja angel?")

The implication being that Sam's soul is burnt up and the atoms scattered, along with everything that makes him Sam.

I don't see that implication. We've been told so little about souls in the Supernatural verse, that I was almost surprised that Crowley could just *have* Bobby's. I mean, where is it? If they kill Crowley, does Bobby just keep on existing fine? But can't go to Heaven when he dies?

My assumption about Sam is that he would be suppressed as long as Lucifer maintained possession. And that there is no known way to get an angel to evacuate their vessel, so it's a lost cause. But they've never told us what happens to any souls, just what happens to the person. And with Bobby doing apparently fine without his soul right now, it's hard for me to tell how those are related.

Also, the Buffyverse is confusing me.

eta: Yes, God reconstituted Cas, as well as teleported the boys.

Also, the Buffyverse is confusing me.

The Buffyverse doesn't really follow strict laws of logic, so you're likely to give yourself a headache if you try to impose them.

Crossroads demons don't collect on the bargain till the agreed on time period is up, and the person dies.

The people in Crossroads lived the ten years of their bargains just fine, souls in place, but with a lien. Dean lived for a year. The soul doesn't go anywhere until the deal is up, and the person dies.

The soul doesn't go anywhere until the deal is up

But Crowley has the soul now. That's why I'm confused.

Crowley: I fully intend to give it back.
Dean: Well then give it back!
Crowley: I will.
Dean: Now!

So what does that actually mean about/for Bobby?

I'm beginning to think the Buffyverse might make more sense than this.

The implication in S3 was that the demon holding the contract could make it null and void (and in S2, we see that they could do that without undoing the granted desires). So Crowley could release the lien on the soul. My impression is that Crowley has soul rights via contract, not the physical possession, and that the writing was a little fuzzy there.

I think he has a lien on the soul. Like buying a car. Technically it's the banks until you pay it off, but you can drive it.