Not too long ago, we had a little bit of a cold snap, and since most of my plants are still young, I brought them inside for the week...when I suddenly had an explosion of house fly population (killed 8 one night and woke up to 12 new ones buzzing about) So I moved everything back outside and the flies disappeared.

I've checked the sage numerous times and cant find much of anything in large numbers. I've found a few small red/white colored things that are nestled in the crook where some of the leaves meet the stem. and there have been a few spider web like things attached close to the stems as well.
Any idea what it is? and what I can do to get rid of them w/o chemicals that cost more than a poor student can afford?

I'd start by taking the whole plant, turning it on its side (with some plastic around the pot to keep the soil from spilling out), and running it under the faucet, leaves, stems and all. Also check to make sure there are no eggs underneath the leaves. Repeat every couple of weeks for a month or two.