There are two good options that I know of.
Noteworthy Composer is a nice scoring application, although it lacks some of the features of expensive high end programs. You can still produce perfectly usable scores with it though. The trial version is free, but is has some limitations, mainly on the number of times you can save and what you can print along with your score. The full version is cheap though.
The other good one is
Lilypond. Take a look that their essay and at the manual. It's free software, as in price and as in freedom, which is always a plus. It should be able to produce almost any notation you want. It differs from most notation software in that it has no graphical interface. Instead, you produce your scores by typing in a description of the music into your favorite text editor and rendering it with Lilypond. It sounds intimidating if you're not used to it, but it's not as hard as it sounds. For many people that's a big selling point. Producing a score for a single bass is pretty simple, although scoring for an entire orchestra is a little more complex. You can see
some examples of scores produced in Lilypond along with their sources at the Mutopia Project. Lilypond is my first choice for scoring.
Both of theese programs can produce scores and MIDI files, but I think Noteworthy Composer can only save its scores in its own format, which is a minus. Lilypond produces scores in many formats, PDF usually being the most useful.
