I'm actually working on personal one myself covering 25 systems, and yes it is a long and frustrating process. If it was my job to research pricing it's be a liitle better, but as video games are a hobby, the time needed for a task of this nature can be hard to come by.
Other problems arise with specific systems such as the pre crash systems in the fact that for the most part are harder to come by locally, and usually found in garage sales, goodwil, etc. Just cause you fouund a quadrun at a garage sale for 25c doesn't mean that's it's market value. Thus you turn to ebay completed auctions and message boards, which do give you a descent average to work with. The problem with ebay and such though is that it can takes years to get enough completed auctions to have a good representitive price on pre-crash games. For example, put coleco in ebay and you get 300 results, put nes and you get nearly 20,000. Even pricing colecovision R2's can be hard if only 2 sell and one sold for 3.99+ Shipping and anther sold for .99. Intellivsion is much like this also. Odyessy 2 is worse yet as most games are sold in lots, as opposed to singlely.
Another major problem that arises is variations, the 2600 has a lot of variations, and there is a market for major variations. The question though comes down to which to include/exclude and being able to research them indepently.
As opposed to previously published guides, I've been attempting to also lists prices for complete games, which has made my attempt at a guide even harder, in that I've had to research which games came with overlays, etc and also run into the pre-crash problem again. Will all complete copies of Gust Buster go for $230? or will it be $100 next time or $500?....these games just don't come up very often in this condition.
Overall, I've been working on this for 4-5 years and I have be able to pinned down most titles pretty well, but even in the time since I started collecting data, I've had to revise my pricing(granted it's easier to reivse then to research from scratch).
For guides out there, Atariage, seems to be the best for atari rarity, (Granted not perfect_ big props to the variation attention, digital press is probably the most complete for all systems, though their Turbo Grafx section seems terribly priced to me. (Their online guide has adjusted these a bit). I applaude Video Game Collector for attempting to do this monthly, though it seems that not all the games or systems are researched monthly.
There is a new SNES guide available from snescentral.com, that is pretty good (released 8/2006)
Ideally I think a yearly publication would surfice, whith multiple people each concentrating on a specific system or systems using a common research method. Until then, Atariage, Digitpress, VGC, internet guides, adn personal research is the best you can hope for.