If you want a faster sampling rate, how about repeatedly calling analogRead in loop instead of using an interrupt?
I used the timer/interrupt setup so that eventually the user can set the sampling rate to some arbitrary number (1kHz, 5kHz, 10kHz, etc) and have it be somewhat accurate. Hopefully this will mimic the behavior of a 'real' oscilloscope better.
Plus it was an excuse to learn how to do interrupts. 
nice work, really love this idea. wish i had the skills to help you with it.
i tried your setup with a standard IR receiver module but can't see any results. any ideas?
It runs on 38khz. Maybe that's too fast?
For the sake of simplicity I pinned the sampling rate at 5kHz until the serial interface with Processing works a bit better, so I imagine that might be one problem. Also, there is a scaling issue where values of 5V and 0V don't display correctly - if your module is flipping between those two points rapidly you might just see some vertical lines.
Hopefully I can fix some of these things when I get a bit of time to play with it again, check back in a week or so and it may be working better.