Keep in mind I am still new (less than a year) to ebay, but in my opinion it depends on what you are selling. Remember that your store items will only show up in an ebay search if there are only a few listed at auction, or if the buyer specifically searches for buy it now or store items. For example, if you are selling something that when you search for it there are thousands of items found, it will be harder for the buyer to come across your item in a basic search. I sell a variety of things, a virtual yard sale type thing... but if you are selling the same thing all the time I have another suggestion. A friend of mine sells one item and has a store. What she does is keep one or two at auction all the time, and mention in the auction something like "If you don't want to wait for this auction to end, check my store where I have many more for a buy it now price!"
The listing fees are less, but the final value fee is more so about the cost effective part you would have to take into account the final value of your items.
I do have a store also and what I tend to do is list my items at auction for at least two times (more if they get lots of watcher/hits) and if it doesn't sell I just put it in my store. I figure if I have it sitting on a shelf it won't make any money at all so any chance is better than none. So far it has worked out pretty good. I haven't had any months yet where my sales from the store haven't covered the cost.
Hope this helps and isn't just a bunch of useless babble... I tend to do that sometimes .