Hi!
So I've done a lot of experimentation with the arduino, and I think it's taught me enough at this point that I can justify designing and making my own specialized PCBs with all the specific hardware I need and a different AVR microcontroller with more I/O and speed. I'm in the home stretch of getting the basics of my project down 
But I still need a way to program the AVR while it is on the PCB.
If I use this usb to parallel adapter, here: Link Depot Model USB-PRINT 9.8ft USB to PRINT Cable - Newegg.com
and this programmer schematic, here: captain.at - captain Resources and Information.
then I should be ok, right?
Are there AVRs this won't work for? What do I have to look at in the datasheet to see if it is compatible with this method of programming?
I'll miss the days of pressing Verify and Upload to I/O Board, but I'm excited about completing this project, too ;D
EDIT: I decided overnight to use the Atmega128.
EDIT: I found this Simplest 128 atmega programmer - Do It Easy With ScienceProg which seems to indicate it's possible. Thanks everyone! I'll shut up now :-X