I've attempted (and failed) this once before, but after recently discovering that I was missing two cards from a team set I thought I had finished, I am now determined to finish the arduous task.
You see, when I got back into the hobby in '09 I started using the TeamSets4U website that lists team sets by year and product. It seemed like it was pretty thorough and so I would consult their site when putting together my want lists. All was fine and dandy until I saw a card on eBay that I knew was not a part of my collection. Since I began the inventory process I've discovered other cards that were missing (not to mention cards that I have that were not on the website's list) and so this has given me a chance to get a better idea of what needs to be cataloged.
The importance of using multiple sources for gathering information during this process can't be emphasized enough, as another website I've been using during this process- Beckett- has also been found to be missing cards from team listings. Because of these oversites, I've decided to also run searches on eBay and Check Out My Cards to see if any other items receive hits.
Like I said, it is an arduous task; but for a completist like myself, it is well worth the time invested.