Looking at the patch notes from last night, it appears that the missing glyphs are still missing (writing this over lunch at work). Good news for me - I still have too many glyphs of mage armor. I am currently selling these at 350g Alliance side, and 250g Horde side, subject to demand and supply. At various times, I advertise them in trade "Glyph of Mage Armor in AH. Very limited supply (Scribes can not make any more)". Taking an each way bet about when Blizzard will fix this, over a 3 week period, it is my intention to only have 5 of these, selling the rest before Cata.
Herbs are now available. Not at old prices, but getting there. I buy ink (generally from Wek), but I am now squeezing him down to 2g50 per ink (either snowfall or ink of the sea). He balked at the new prices, but that is where I think they are heading. I have a moderate stockpile of inks (1.5 guild bank tabs), looking to fill up to 3 tabs with cheap inks between now and Cata. On that note, remember to convert the majority of ink of the sea down to a mix other inks between now and Cata, as it appears that Jessica will only play nice until then.
I am planning to sit on the snowfall ink to sell after Cata, and will be content to carry up to one guild bank tab of them.
I am currently pricing inks at 5g (a small discount on the AH), with re-crafting costs of about 16g. With a couple of exceptions I post daily with a 21g threshold 90g fallback, 2 each, 48 hours, no autofallback; pulling 2.5-3K in daily sales. I intend to tweak this further.
I want to hit Cataclysm with 20 of each glyph - down from my pre-patch levels of 40 (the reason I still have mage armor), and I will be discounting some glyphs that have not sold down to replacement costs (at the moment 16g). I really should set up high sales and no/low sales glyphs as seperate groups, but the Auction Profit Master UI for sorting glyphs is painful (as was QA3 before it).
Finally, keep an eye on inks other than Ink of the sea. There are not many around, but every so often I see good prices for 'lesser' inks, buying them when I do.