Your time is not free: Opportunity Costs

"I can charge less for glyphs because I farm my own herbs, so they're free".

That sentence is the bane of many rational marketeers' existences. Your time is not free. No matter how you actually acquired the herbs, the simple fact is, you could have just sold them on the AH instead of milling them. At the very least, consider how many dailies you could have done in the time it took you to farm those herbs. Multiply that number by 13g or so, and call that your baseline minimum wage, since as Fizzle pointed out, you could have been doing easy dailies instead.

That's opportunity cost in a nutshell. How much could you have made selling those materials instead of turning them into a crafted good? This applies to farming as well as other modes of acquiring materials (I do a combination of paying farmers to herb and buying cheap herbs in bulk when they show up in the AH).

If you bought herbs at 50s per because you have a good supplier, and they currently sell for 1g50s per on the open market, consider selling the raw herbs instead of the glyphs. Take a good hard look at the expected profit per glyph you can get. It might be that you'll get more profit for those herbs by making flasks. It might be that you'll get more profit selling the herbs back on the AH. It might be that inks are selling well right now.

Personally, I like to spread risk around (diversify!), so if I get a crapton of cheap herbs, I'll make some flasks, make some glyphs, and if the market condition is right, I'll sell the herbs back on the AH.