“He should have done it” is known to have the meaning, “He was supposed to do it, but he did not.”

But in the following passages, the “should have done” seems to mean something different.

The meaning of “He should have done it” in the following passages seem to be “He actually did/had done it”.

Am I thinking wrong?

Here are some examples… 

If anyone was too good to die, it was Jesus. If anyone should have done greater things than walking dusty roads and talking with people too dense to understand him, it was Jesus. http://girltalk.blogs.com/  

-----> “If anyone should have done greater things” seems to mean “If anyone had done greater things”

If Y2K should have done one thing it would be to teach customers the dangers of being tied to a software provider who could say "oh yes we know, tough ***, upgrade for $1M". I'm not sure it did.

http://it.slashdot.org/article.pl?sid=05/01/05/0216220&from=rss 

-----> If Y2K should have done one thing  = If Y2K had done one thing

If he should have done this, they would praise him.

http://www.baylor.edu/content/services/document.php/54372.pdf  

------> If he should have done this,  = If he had done this

No - what she did get (not any more then) was a big and clearly stated warning that the account was going to be renewed and a link to where she could go and "renew it". Now if she should have done so - would we have been charged twice? Would she have received an oridnary account or what?

http://discussions.apple.com/message.jspa?messageID=3182386  

------> if she should have done so = if she had done so

If you should see her, tell her I miss her = If you see her, tell her I miss her

If he should try to sue me, he'll regret it = If he tries to sue me, he'll regret it

And, as you say,

Now if she should have done so - would we have been charged twice? = If she had done so ...

If he should have done this, they would praise him. = If he had done this, they would praise him.

As far as your other examples are concerned:

If Y2K should have done one thing it would be to teach customers the dangers of being tied to a software provider who could say "oh yes we know, tough ***, upgrade for $1M". I'm not sure it did.

To me, this has the "ought to" meaning: Y2K ought to have done this, but it probably didn't. I'm inclined to this interpretation because of "I'm not sure it did", and also because the rest of the sentence is not written in the formal/old-fashioned style that I'd expect from someone using "should have done" in the other sense.

If anyone was too good to die, it was Jesus. If anyone should have done greater things than walking dusty roads and talking with people too dense to understand him, it was Jesus.

I'm not sure what the author means here. I naturally read the "ought to" meaning: he ought to have done greater things, but he didn't. But it seems an odd thing to say. 

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I'm not sure what the author means here. I naturally read the "ought to" meaning: he ought to have done greater things, but he didn't. But it seems an odd thing to say.

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I agree it's the  "ought to" meaning. According to the destiny/fate perhaps, he/Jesus ought to have done greater things, (but his fate destiny/changed because of the people/mortals???).  Not that strange to me.

You're right about the end, but the first part should be:

 If anyone ought to have done greater things than walking dusty roads and talking with people too dense to understand him, it was Jesus."

or:

 If anyone had [past for must] to do  greater things than walking dusty roads and talking with people too dense to understand him, it was Jesus."

thus this should have has the meaning ought to have/had to  

This is present/future, not past.

If he does that kind of thing, he will meet so and so consequences. [perfectly OK

If you want to put more doubt on him doing that try:

If he were to do that kind of thing, he will meet so and so consequences.

Were he to do that kind of thing, he will meet so and so consequences.

This is all present/future time, not past.  Perhaps Mr. Wordy has other suggestions.

BTW, were is allowed in if clauses.