If you want a rip to archive a valuable CD then use EAC and rip to a CUE file. Ripping to a CUE file using EAC gets all of the data that is on the CD (including any pre-gap that may be there for track 1). If you ever lose the CD or want to make a copy to play in the car or at a head-fi meet you can burn a copy using the CUE file and get an exact copy with all of the gaps correct.
If you rip to separate tracks you lose the pre-gap data for track 1. Standard ripping protocol is to append pre-gap data to the end of the previous track. So pre-gap info for track 2 gets appended to the end of track 1. Unfortunately there is no track 0 so if track 1 happens to have pre-gap info that info gets lost.
Most of the time any pre-gap info is silence. However on live CDs the pre-gap may include actual audio like audience cheering or an introduction to the song.
So to be paranoid that you are getting all audio info for a CD for archiving you should rip to a CUE file. A CUE file also makes it easier to burn a copy of the CD.
You can use various tools to later split the CUE file to separate tracks. Foobar will do it. Just load the CUE file and convert the files to FLAC or your favorite format. Unfortunately you lose pre-gap info for track 1 doing it that way.
A better CUE splitting tool is
CUETools. Scroll down to the bottom of the Wiki page to get the 1.9.5 development version which has the ability to verify the CUE file using AccurateRip. CUETools will split out a separate track for any pre-gap that is on track 1 if track 1 happens to have pre-gap. You can listen to that (usually very very very short) file to see if the pre-gap is anything other than silence. If it is actual audio you can decide what to do.
Configure CUETools with:
Audio Output: FLAC or your favorite format
CUE Style: Gaps Appended
AccurateRip: Encode and verify
The AccurateRip feature is really cool because it is able to verify the accurate rip info even if you have a different pressing than what is in the AccurateRip database. It does that by calculating various offsets and checking for a match. EAC will sometimes tell you that it was unable to verify any of the tracks with AccurateRip because you may have a different pressing. When that happens you can use CUETools to verify the CUE file against AccurateRip. Pretty cool.