I'll give the input that I am pretty sure about.
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[ ]Fill up missing offset samples with silence (*** says check- others say NO, which one?)
[ ]No use of null samples for CRC calculations (*** says check- others say NO, which one?)
If you are using the proper read offset you would want the first unchecked, since there won't be any missing offset samples.
Using null samples for CRC can be checked if you like, mainly it's to make sure you not using silence to compare CRC's, which even on a bad rip would give the same CRC. If it's that questionable and you are that concerned you'd want a new cd. So it's really a matter of how concerned you are about crc's, I use md5sums though if I am concerned.
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[ ]Delete leading and trailing silent blocks (*** says check- others say NO, which one?)
I don't advise checking this if you after a 1:1 copy of a disc. The idea would be to keep everything from the original CD and checking this I think would compromise that.
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[X] Overread into lead-in and lead-out data (*** says check- others say NO, which one?)
In order to over-read into the area the area that the read-offset would require. If you had a read offset of +120 you'd need to be able to over 120 samples somwhere in order to get all of the track, although there would be no audible difference, 120 samples will be missing on the last track (or is it the first?). Note that not all drives can over read though. If you drive is unabe to do so you'll get a read or sync error at the end of a cd. I believe EAC needs to be restarted in order for the option to take affect as well. Over reading is required to get a 1:1 copy.
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Gap/Index retreval method: Method A (I have no idea how to determine which to use, but Im using A)
It depends on the drive, some can't use method A.
I'd also like to point out that disabling C2 correction is also recommended since a lot of drives report they can use it but don't do so very well. Also checking "Drive caches..." is also recommended even if a drive does not. It will not affect drives that do not cache, and it extremely god on drives that do.

Anything else your curious about?