HD signal output? Moto 6200 + 1024x768 Plasma

All you can do is try it both ways to see what you think is best.

I have a 6200 and a Panasonic TH-50PX60U and currently have the STB set to 1080i and connected via DVI>HDMI.

However, I'll probably reconnect the component cables because I think the picture on non-HD digital channels is better via component than DVI/HDMI.

I prefer the TV's internal tuner for analog channels, the component connections from STB for non-HD digital channels, and the STB DVI output for the HD digital channels.

If you send 1280x720 720p the your TV has a much easire job of rescaling in to 1024 x768 since it does not have to de-interlace it and it just has to eliminate a out of every 5 pixels in each row to get from 1280 to 1024 and then insert a new invented row about every 15 rows to get from 720 rows to 768 rows.
If you send 1080i the the TV has to first de-interlace it from 1080i to 1080p and then apply motion compensation which involves a lot more signal processing then 720p and then eliminate almost every other pixel per row to get from 1910 to 1024 pix3ls per row and it has to elimnate about 1 out of every 4 rows to get from 1080 rows to 768 rows.
You just have to try each resolution and determine if it is better to have your STB do some of the rescaling or to have the TV do it all.
If you watch mostly 1080i HD programs you are probably better off sending 1080i. However if you watch mostly 720p HD programs (ABC, FOX and ESPN) then you are probably better off sending 720p. And for SD analog or digital programs you are best off setting the 4:3 override output to 480i.