When you mention pages linking in are you wondering why they don't show up on google? If that is your question, it's probably because their page rank is not high enough. They have to have a rank of 3 or 4. You can check links across several engines at:
http://www.freewebsubmission.com/link-popularity.html
some of the other ses may have more links because it does not matter to them what the
pr is.
Re: "I've noticed Google has not indexed any pages below the main front page". I took a look at your source and everything looks good so they should be back shortly. Sometimes a lack of doc tags can delay things. I noticed you have robots tag in there as well. Be patient and submit to more directorys. Go to:
http://www.usnet.tk/
and rip down the left side dirs and ses submissions. That will work.
peace...Paul