I very often get asked about which score writing software I recommend.  Personally I have my favorites depending on whether it's personal use, composing, arranging, young pupils, advanced pupils etc.  I will try to give a roundup of what is available so you can make up your own mind.

There are two broad kinds of software on the market :
1.  Sequencers which have score editors on-board.
The market leaders here are Cubase score and E-magic Logic.  There are  cut down versions called respectively, Cubasis and Micrologic.  Both are excellent and there is not much to choose between them.  It must be borne in mind that these are sequencers first and foremost.  You can get very good results from the score editing features if you persevere, but it has to be said that the scorewriting facilities of both are difficult to get to grips with.  My pupils use Micrologic for inputting notes and doing arrangements, then they save the file as a MIDI file (which any music software can understand) and load it into a proper scorewriter.  Inevitably it needs editing heavily, but if you've been reasonably accurate, then there's not much work to do.  Often, clefs are wrong and need altering.  Note lengths may need some attention also.

2.  Scorwriters which have some sequencing capabilities.
The main software available is Passport Encore, and its cut down version Passport Musictime, Coda Finale, and Sibelius, which was previously only available on the Acorn but is not out for the PC and Mac.  There are other, cheaper versions around, of which I've had a detailed look at Music Works by Middle Earth software.
Coda Finale has an excellent output but is a little difficult to use at first, so many people get put off it soon.  If you persevere, however it is worth it.  Younger pupils find it very difficult to use and many lack the patience to get it working properly.
Passport, I understand have gone out of business, so I don't know if you can get the software any more.  Their software is outstanding and very simple to use.  You can get excellent results very quickly and the young pupils get on with it very well.  Encore can produce up to 64 staves but Musictime only 16.  Individual part extraction is available on Encore but not Musictime.  Final score formatting is difficult and nowhere near as easy as Sibelius, so this takes time, even for an advanced user.  My pupils always ask for my help in formatting.  Staves can be displayed in colours and so can individual notes.  Score output of the printer is excellent.

Music Works is a very cost effective option for those on a budget.  Unlike any other scorewriter I've seen, this allows you to put more than the 'allowed' number of beats in a bar, for example you could put 5 or more beats in a bar of 4/4.  This has obvious disadvantages with pupils.  Beaming is not automatic, and quavers are printed individually.  You then have to select the appropriate tool to beam them.  The interface is fairly simple (but not as simple as MusicTime or Encore) and the standard of printout is very good.  Colour display and printing of staves is possible.  One feature of Music Works which is unique and very useful, is the ability to copy the page and paste it into other applications.  For teachers this is an excellent tool for creating worksheets or for pupils to create projects with musical examples.  The only way to do this on other music programs is to hit the print screen key, paste into an art program, crop it and save it as a graphics file - very long winded!

Sibelius offers pre defined manuscripts so that you can see what the manuscript looks like.  The page is already formatted which is a huge advantage.  The interface is innovative in that you are looking at your pages on the screen as it would look like when you print it.  Personally, this is a disadvantage because you are forever turning pages and I can only work at Sibelius for about an hour before feeling quite nauseous.  Many arrangers I've spoken to however, like this interface.  The old C-Lab notator on the Atari got it right, because there was a choice of linear view or page view (as there is on Encore).  With a single click you can switch between concert C score and transposed score.  Copying and pasting parts is effortless and very accurate - unlike Encore which often corrupts the information in the clipboard, so when you paste it looks nothing like the passage you copied.
The big minus for Sibelius is real time input from a MIDI keyboard.  No matter how accurately you play, the note lengths are often inaccurate interpreting, for example straight played quavers as semiquaver, semiquaver rest.  Score output is outstanding with a choice of fonts even!  Older pupils who are very au fait with notation get on with it very well, but with young pupils, results are limited.

For each program, I loaded a MIDI file of Boccherini's famous quintet.  There is a printout of the quintet from bar 29 for each program and also a saved MIDI file that the program created.  Some programs reproduced the original MIDI file very well, whereas others distorted them.
 

Here is the original MIDI file of the Boccherini quintet 

Passport MusicTime / Encore

Beaming not intelligently handled.  Rests missed.  Incorrect number of notes in a bar.  Accidentals repeated within the bar.  Stem directions incorrect.  Melody has incorrect note lengths.

For this test, I played in a 5 part arrangement of 'Yellow Bird' into a Logic sequencer and quantised it perfectly. This was saved as a MIDI file and opened in the scorewriter program.  From here the 5 part arrangement was edited to include the following parts :

Passport Music Time
Handled the transfer from MIDI very well.  Minimal editing was required. Transposing parts were easily done if you had a reasonable knowledge of music theory - just select the stave and select the transpose part to the new key.  Layout of the score was a little tricky and took around 15 minutes to get to a satisfactory outcome, which was really trial and error with systems per page, size of score and measures per system.  Part extraction is not possible on Music time, but it was possible to erase all staves except one and print that one.  You then have to return to the saved version, erase all except the next, print and so on - a rather long winded approach.
Total time taken from import to printout of all parts : 35 mins

Passport Encore
This was exactly the same process as Music Time, except part extraction was possible.  Also, all the headers are treated as a separate global function, not as individual text objects, so it was not necessary to re-type it for all the parts.  Formatting is a bit of a pain.  For example, if you reduce the size of the score to (say) 75%, then extract a part, that part won't automatically go down to 75%, you have to reduce it again.  Transposing instruments were a little tricky.
Total time taken from import to printout of all parts : 24 mins

Sibelius
The imported MIDI file was badly distorted, and in many places needed erasing completely and step entering.  This took an awful long time.  Once the piece was actually in, it was a breeze to transpose and replicate parts.  Layout was automatic and very stylish.  Transposition of transposing instruments was simplicity itself - you don't have to think about how far up or down it goes - the program does it all automatically.  Scores can be presented in concert pitch or transposing at the click of a button.  Part extraction again was incredibly easy.
Total time taken from import to printout of all parts : 56 mins

Coda Finale
The imported MIDI file was well transferred.  Very little editing was required.  Layout was very simple and mostly automatic, although my computer seemed to stop working for around 20 seconds every time I asked Finale  to do something complex, like extract a part - this indicates that the program does put quite a load on the processor and memory.  Part printing was very easy and so was transposition of parts.  Interface was a bit tricky to get used to.  The linear view of the score was fabulous to work with - much easier than the page view of Sibelius. - and  it is switchable between page view and linear view!
Total time taken from import to printout of all parts : 28 mins

Music Works
The imported MIDI file was a total disaster.  The huge editing task began with selecting small areas (as it recommends in the manual) and selected the auto format function, which went some way to it looking like 'Yellow Bird'.  Many parts, though had to be step input all over again. Part extraction and transposition of parts was not easy.
Total time taken from import to printout of all parts : I gave up after 1 hour 15 minutes.

For this test, I played 'Dixie' (especially for all you yanks that like this site!) into the scorewriter.  They were played in exactly the same way into each program.  No comments, this is how it turned out.

I'm not going to recommend any particular package, since it really is horses for courses.  None of the packages available at the moment is ideal in every way - that is for certain.  It is, frankly, very disappointing that a decade ago we were all using the excellent C-Lab notator on the old Atari computer which gave perfect quantising, extraction of parts, linear and page preview mode and easy formatting.  The obvious drawbacks were the relatively poor standard of print (compared to today) and the fact that there was no hard disc involved in any of the process!

Sibelius is the most expensive, and I would argue, overpriced package.  The on-screen help is laughably poor, so the user has to resort to the lengthy manual.  Handling of different voices on a single stave is unusual.  For example, if you have a group of thirds which you want to split into two voices, you simply can't do it by assigning voices in the usual way...It will let you swap all the notes to another voice but   incredibly, the program won't let you select a group of notes and assign them to a particular voice. Simple things like changing the speed of the click is very difficult to do.  If you write a tempo indication (e.g. Andante), it will click at the appropriate speed, but, the count-in is played at the default speed so you get a count in at 120 BPM and suddenly a slower beat at bar 1 - what a joke!  Incredibly, to get round this problem you have to place the text before bar 1 to get the count in at the appropriate speed.  Sibelius is full of these annoying little glitches that just frustrate the user.  I've met a lot of 'serious' musicians that have been very excited by public demonstrations of Sibelius and they are all very eager to part with their hard earned cash to get this thing.  It is, of course, aimed at the 'serious' classically trained art musician with its page-like screen view, suitably 'pop music is for plebs' title and avoidance of technical language (like 'record' and 'quantise') to appeal to the technophobe.

There is a fabulous little plug-in bundled with Sibelius which enables you to publish scores on the web. I hope this catches on, since it really gives internet music a whole new meaning.

Passport Encore seems to have an annoying habit of corrupting data when you cut and paste.  After a few attempts, it does it correctly.  Formatting is difficult with Encore to say the least.  You have to manually specify how many systems per page and how many measures per system, then decide on the size of your score.  Incredibly, when you extract parts, it doesn't remember the page size so you have to do it all over again - what a bore!  Empty bars crop up all over the place in the course of editing.  Note ties over pages can't be done, unless you are in linear view mode (very handy).  Selecting whole staves can be a nightmare.  You have to click twice at the beginning of the stave.  The problem is, you can very easily just click once, which selects the stave on the current page, only it looks like it has selected the whole stave.  If you then go editing, like changing key etc., you may make yourself a lot of extra work having just inadvertantly edited just one page.  Transposing parts is not easy either.  A frequent mistake is to transpose the key of a part and forget to also transpose the notes.  Once transposed, the MIDI output is also transposed, so playback of a mixed transposed score is impossible.

Coda Finale has the same formatting problems as Encore.  The interface is very difficult to work with and real time recording is not easy with large scores.
Passport Music Time is very cheap compared to Encore, and it has almost as many features!  It also has the same problems.

As for Music Works.... gosh is that the time already...I must be off.