I've just been using the brewtility.com recipe calculator. It's pretty good for being free, online, and will save all your recipes. The one downside is that you have to register on the site to use it. Registering isn't bad, though, because you can share recipes with other people, look at public recipes, or use their forum to ask questions (though the forum doesn't get a lot of usage).
Here's a screenshot of the recipe formulation page:
It lets you adjust things like your efficiency, batch size, boil size, boil time, and mash temp (if you're using an "all-grain" recipe type). Those adjustments will then be reflected in the recipe calculations. In your profile, you can adjust your IBU formula and your measurement units.
The ingredient list is fairly large and you can approximate different types of ingredients if those ingredients don't match (by adjusting Lovibond, grain-sugar extractions, and alpha-acid ratings).
It works well for me, anyway.