We've been doing production programming for years with the MKII and custom scripts with AVRDUDE (mostly to burn a serial number automatically). It worked great for a long time, but these MKii's are starting to flake out, and are no longer being manufactured. I'm uncertain if the clones will work reliably.
What's the go-to programmer these days that's reliable, and plays well with avrdude? We'll be using atmega328, sometimes the -p and/or -pb variants. 6 pin ISP header on-board for in-system programming, 3.3V. Cost really isn't an issue. Probably windows XP if that matters, but we can get a new PC for Win10 if it helps. Thanks!