Sure, there are other notation programs out there for you to use, but the two big names remain: Finale and Sibelius. Which one do you prefer (include version . . . e.g. 2007, 2005, etc. for Finale or 3, 4, 5, etc. for Sibelius), and why?

Sibelius, all day every day!

Any particular reason?

Other than the included copy of VDL, I'm a creature of habit and I used Sibelius long before I even touched Finale. The same is true for most Finale users who have tested Sibelius. If I actually invested the time to learn Finale and all of it's bells and whistles I might actually prefer it to Sibelius but I don't see that happening any time soon.

I use Finale for most of my stuff. (this is what I learned to use first) However, if I'm writing for percussion I usually use Sibelius because it sounds better for percussion and makes more sense for percussion writing.

P.S.
I use Finale 2006 and Sibelius 4.

Try Sibelius 5, you don't be disappointed!