For quite a while I used Tabledit -- $50 for the full version, available online only. It's ostensibly a "tab" program, but it's better implemented for classical notation than a lot of the over-the-counter tab programs I've seen.
You can do your note entry from the staff system instead of the tab system, and completely supress the tab system if you so desire. Note entry is basically "free hand," so you can freely group and stem notes any way you like and notate three or more voices or "layers" on a single staff (most tab programs are limited to two layers only). It also has a fairly good selection of classical and classical-guitar specific symbols. It's clear the creators knew something about classical guitar and kept us in mind as they developed the software.
True, it doesn't have the myriad of styles, fonts and typesetting options that the pro notation programs have. It' looks a little clunky, but it's quite easy to read and, as I said, has a lot of features with the classical guitarist in mind.
It hasn't been updated for a while, but it's still supported and there is a very active community forum devoted to the program. Check it out -- for the price of a video game, it's definitely a good value. A free trial version is available.
I'm using Sibeleus these days, but here are a couple of old scores I uploaded here that were created with Tabledit.viewtopic.php?f=12&t=25189viewtopic.php?f=12&t=25306