Electronic – What kind of JTAG connector is this

There are sockets available for both DIP packages and SMD packages. No matter which direction you take, I would suggest using a socket. That way, if you let the smoke out, replacing the chip doesn't require desoldering and resoldering.

The choice between DIP and SMD is all about what you are more comfortable with. There is typically a larger variety of microcontrollers available in SMD. But they are also more fragile. Especially when used with a socket. If you're taking the chip in and out a lot, you will most likely bend or break some pins. The pins on a DIP are much more forgiving in this respect.

It's rare that you'll find someone taking a chip out of circuit and placing it in an off-board programmer these days. I had to do it with old school PROMs in college. But I haven't done it since. You are much better off having the JTAG on the board itself. @i.amniels mentioned in-circuit debugging being a huge advantage. I will echo that sentiment as it cannot be said enough.

There are many different JTAG connector configurations. The AVR one uses 10 pins. And you really don't have a lot of say in the footprint of the header you can choose. You have to match the pin size and pitch to your JTAGICE. Atmel has a recommendation for the part number to use to interface to the JTAGICE. I would just stick with that.

http://support.atmel.com/bin/customer.exe?=&action=viewKbEntry&id=2

Assuming the processor you are referring to has boundary-scan cells behind the pins that are connected to the Flash device you want to program, you should be able to program the Flash with JTAG/boundary scan without involvement of the processor's core. There are also some other JTAG based programming methodologies that can help to speed up the programming compared to boundary-scan based Flash programming (which is relatively slow).