We tried the software a couple years back, and didn't enjoy it at all. It was easy to set up, and we did have a projection on the wall, which was nice, but it just didn't have the same feeling of walking up to the big board and putting on the sticker of your new fantasy stud (or dud). The cost of the board works out to about $5 a team, so if you haven't used one yet, I suggest you DEFINITELY try it out. The colour coded stickers (by player position), make it really easy to track every owner's picks and needs.
To clarify about our league's draft day setup, the bottom 3 teams pay for the food at the draft, and we do a draft lottery so the team that finishes 10th, has more chances at picking #1 than the 11th or 12th place teams. Buying the food keeps teams from totally tanking to get that top spot, and by having a weighted lottery, it pretty much guarantees teams won't lose on purpose for a better shot next year.
Go buy a board! We've used FJ Fantasy every year, and their customer service is top notch.