Personally I don't care too much if my pages are indexed. I care more about my pages getting traffic. So I usally pay more attention to my analytics and log files to identify which pages generate traffic and which ones need improvement.
Since you specifically mention checking the index status for Google why not log into Google Webmaster Central?
WMC just gives you the total #, but I'm interested in specific URLs. IMO indexing becomes more important the bigger the site is. When a page gets indexed it opens up to long tail search, even if you don't push that specific page. So if you have several million pages, opening them up to long tail searches will be significant amounts of traffic. Analytics will only tell you which pages are already getting traffic, i.e. they will show what's working to some minimum degree, but it won't show what isn't working at all.
Analytics will tell you pages that get traffic AND pages that dont get traffic. Simply compare the pages that have traffic according to your analytics to your master URL file. The urls with no matches are the ones that get no traffic and need some extra attention.
Based on my experience I do agree that long tail is powerful and can be extremely profitable. I also have found that sometimes it is actually better to not work towards getting 100% of the large websites indexed. Sometimes a bit of pruning will lead to significantly higher profits at least that is what I have discovered over the years.