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Consider the following sentence:

We consider a simple protocol as the base configuration and compare with it three other cases.

Which one is more correct, "compare with it" or "compare it with"?

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Compare it with three other cases

is the more common expression.

Compare with it three other cases

is a rewriting of

Compare three other cases with it

and is also correct but not so commonly used.

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"Compare it with" is the correct word order for your sentence, therefore:

We consider a simple protocol as the base configuration and compare it with three other cases.

You also ask: "What do I compare this with?" or "What do I compare this to?"

That is the case when you're talking about the thing being compared.

On the other hand, and this not your case, if you were talking about the comparator itself (the tool of comparison), you would swap them, therefore this would be correct:

This is the tool for comparison. Let's compare with it. Let's start doing comparison with it.

As you can see, in this sentence, you're not talking about 2 different things being compared, but rather about the tool you are going to use to do the comparison.

EDIT: Providing an example of usage:

You have 2 objects different in sizes. You have to compare object A with object B. You will compare with a ruler which will be provided.

Now I simply take the sentence "compare object A with object B" and replace object A with "it":

Compare it with object B.

Now I take the sentence "compare with a ruler" and replace ruler with "it":

Compare with it.

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My case is quite similar to the latter one you mentioned. I am considering a "base configuration" as a sort of measurement tool. Then, I compare the three other cases with the "base configuration". What do you think now? – Helium Nov 24 '11 at 1:35
@Mohsen: I'm not exactly sure as I don't know enough context, but I will edit my answer to provide an example which will hopefully help you decide. If not, comment again. – RiMMER Nov 24 '11 at 1:36
@Mohsen: edited. Tell me whether it helps. – RiMMER Nov 24 '11 at 1:40
Thanks RiMMER Ψ. Now, it is clear. – Helium Nov 24 '11 at 3:54

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