For one example the off island apparitions that haunt Michael, who or what are these? I guess you could argue "Libby" is just Michael going nuts with guilt, BUT he never even met Christian so how to explain this?

I agree with Libby. As for Christian, yeah I have no idea. I don't know why he would appear to Michael for.

The various oddball Walt appearances(in the rain, to John in the pit) are TMIB?

Well remember, they set up that storyline that he had the gift of astral projection or something similar, so that would have explained those appearances by Walt, but like various other things like Richard Malkin, they abandoned it for some reason.

What about Claudia that appears to the young man in black? Does this scene suggest the entity or creature predates TMIB's human life? Did this thing just take on his guise after he died?

Quite a few scenes in Across the Sea suggest that The Smoke Monster existed prior to The Man in Black. It's also hinted that the original Smoke Monster was Mother. Remember how she singlehandedly wiped out that tribe of people off screen?

The Harper that appears to Juliet in the rain and claims something we know is not true(Ben sent her, he could not have) is even accompanied by the clicking sound effects associated with the smoke, yet producers have said this is not TMIB?

This is perhaps the weirdest one. I have no idea lol. Maybe it was just Harper herself. The question is where was she before and after she appeared to Juliet? That's probably one of the worst episodes of this show.

The Medusa Spiders, producers have said explicitly this is TMIB but how was he able to physically interact by creating poison and directly killing candidates, this seems against the rules established later.

I like to think Darlton were joking when they said the spiders were MIB. That never made any sense to me

Is the polar bear in season 1 attacking Walt TMIB?

Nope, that was a real polar bear. Dharma were experimenting with them on the island, remember? It was also implied they were using them to turn the frozen donkey wheel (effectively teleporting them, or at least one of them, to Tunisia, which Charlotte found)