re: Best book to begin the Warhammer 40K universe?

tons of great places to start, some suggestions:

Eisenhorn series - spectacular, focuses on inquisitor and his retinue, get a good sampling of his interactions with various races

Gaunt's Ghosts - more standard military sci fi, focusing on a commissar and his unit

Ciaphas Cain - a more action adventure along with some comedy (which is slightly rare in 40k) again focusing on a commissar

Any of the space marine battles / anthologies can be good depending on which faction(s) you like.

Are you more interested in 'good' factions, evil factions? regular humans and their struggles or space marines / aliens etc?

Its a fantastic universe with tons of variety

If you want to go hardcore and get a good idea of the basis of the current events, you can start the horus heresy novels, which are currently running about 60 deep I think, they focus around the huge imperial civil war that took place 10,000 years before the 'current' timeline so ~30k