For serious plotting of thousands, or hundreds of thousands, of deep sky objects, in my opinion there are only two real choices in deep sky charting software:
- MegaStar 5 SkyAtlas
- Guide, version 9.0
MegaStar wins on interface, but Guide wins for the incredible richness of the data that it can bring up for each astronomical object.
Guide is less well known, but it is not expensive, yet it is very accurate and comprehensive (see:
http://www.projectpluto.com )
"TheSkyX" is another similar product that is also in common use, and it also satisfies the requirements of really serious observers , but traditionally its deep sky databases are not as comprehensive as those in the other two softwares that I mentioned.
P.S. I am always up for a discussion of deep sky databases and catalogs. In particular, I know all of the galaxy catalogs, even the highly obscure ones.