I have someone placing links for my sites and reporting which pages he has placed the links. The majority of these pages are not indexed in Google.com, so I am wondering if the links are counted, or are worthless if the page they are on are not in Googles Index? Any help would be greatly appreciated.
I wouldn't say they are worthless as they still help your rankings on other search engines. They might also produce a bit of direct traffic. I don't know if they for sure don't help Google rankings though. Those pages could be in the supplemental index and still help your website in Google.
They help. Reciprocal linking is a natural thing online, friends link to each others web pages and so on. Its just that when you start getting big link pages or a massive ammount of reciprocal links that Google starts to take notice. Thing is that even then, depending on what kind of website you have, they may not care. I've had sites with huge reciprocal pages get high rankings for competitive keywords just because everyone else going for that keyword was doing the same thing.
Check with Yahoo! Site Explorer. If you don't find those links then he is making a fool out of you. If you find them then see the theme of the resources where they are placed. If they are similar to your website then it is good. If not, then also they are bit helpful.