Bee Train still uses cels.

They did Arc the Lad and Noir.

I guess Studio Deen used cels for the Kenshin
Seisouhen OVA. I was pretty sure that Read or
Die was digital.

Last I checked, Sunrise still uses them
too, so if you want some recent robot shows
you're in luck.

Full Digital companies:
Satellite(Arjuna) 
Gainax(FLCL)