Did you try rubbing the brown stuff off? it might be brown algae/diatoms, in which case you can rub it off the plants and they will look nice again.
Yeah, I have tried... With the dwarf sag and crypts it comes off a little but is pretty tenacious... the snail will eat a little from time to time, but (maybe my snail is just picky!) it doesn't seem to go anywhere. I do notice that it hasn't grown much on the newest leaves, though. With the rotala, though, those spots aren't coming off, and on some of them the edges of the leaves are browning and uneven.
Actually, it looks like some of your gravel may have some blue-green algae, too... and your top pic looks like you have some hair algae. Now that I look more closely at the middle pic, you definitely have some blue-green algae on the plants.
I had a lot more of that blue-green algae a week or two ago, but I recently changed from about 3500 --> 6500K lighting, as well as adding Seachem Flourish, and since then it's been on its way out... still a bit here and there though. It's been replaced with the hair algae, though! And that is much harder to remove. Left to its own devices it winds up looking something like green steel wool! Not too sure what to do about it...
Mostly, here's what's most concerning to me:
-The reddish crypt has only put out two new leaves since I got it, over a month ago.
-The green crypt has been slowly growing leaves, but they are staying quite small.
- The new growth on the dwarf sag is pale and almost translucent... I've also heard that the sag and crypts are, in a healthy environment, pretty fast-growing, and these just aren't...
- Excepting the newest growth, the rotalas generally have a yellowish tinge with some brown spotting.
I do have some eco-complete on the way, so hopefully that will solve some of these problems!