If I were to leave a side-panel hole (maple-leaf shaped, if that makes a difference) that was about 2/3 taken up by a fan open the rest of the way (except for modder's mesh), is that gonna be a dust magnet? IOW, should I also cover the rest of the hole with plexi?
Thanks

The problem with a fan hole that doesn't match the fan intake is not so much dust, the fan will take in whatever isn't filtered. The problem is that the un-matched area reduces the effectivness of the fan itself. The plexi should work fine and help you maintain fan performance.

How do you keep dust out in the first place? I look inside my case thats only been together for 6 months and its already getting nappy...

I subscibe to the "Positive Air Pressure" theory. Put just a fraction more CFM into the case then you exhaust out. I should pay more attention to filters as well, but I am too lazy to clean them

you can buy mesh dust filters or aluminum ones. if you don't want them showing on the outside, you can mount them on the other side of the fan but you'll just have to blow your fans and the filter out instead of just the filter.
having filters will lower the cfm pumped and will increase noise slightly from the turbulence.

barring getting filters, you're stuck with cleaning it out often. i think there's some cleaners out there that have anti dust stuff by getting rid of static but dunno how well it will work in a computer

edit: Icpiper posted while I was talking with my roommate. yeah positive CFM will help to as it will prevent dust from coming in the little cracks between everything (unless you sealed off your case except for fan holes then in which case, you should have equal air flow).