I've found that the totem of dawn is pretty good at purifying/improving the aura. I've been stacking them on top of each other, i'm not sure if it improves the effect, but since it's a "totem" maybe it's supposed to be used that way.
Basically what i did is that i have a long column of totems in the middle/back of my tower, and i add more and more as i get more vis crystals to make them. It seems to generate a lot of positive charge, which apparently spills in the nearby chunks and improves the whole area as a result (positive charge generates vis over time it seems).
Also now that i have everything researched, i've been using my reed farm as a primary source of vis, it's really great for that. With a thaumium crucible, arcane furnace below it and 6 bellows, it generates almost only vis, the ratio is somewhere around 90% to 99% vis from items burned.
Any of you tried using a buildcraft quarry with thaumcraft ? i wonder if they pick up the crystals. I've tried using an arcane bore but they require too much micromanagement and i don't want to just sit there next to it waiting.
Edit : oh and by the way if you don't want to use too many crystals, you can duplicate thaumium ingots and enchanted fabric with vis. You can also duplicate ender pearls if you need to make many portable holes. I've also noticed that crystals seem to grow better if you place them in an area where wisps that drop this type of crystal are spawning. But overall i haven't found it to be a good way of farming crystals (it takes WAY too long to get back the 9 crystals you use to make the placeable one) . Killing wisps with a bow or wand seems to be the way to go. Then using whatever type you have the most for basic recipes, and recharging the depleted crystals to get more variety.