I seem to be getting too many quests. I think I have about 25 misc and about 15 main quests. My problem is they never go down.
Whenever I complete one or I am in the middle of one another one pops up. Sometimes I lose track of the story and it can be very annoying.

Anyone have ant tips?

You can click on them to make them active / inactive. Keep only a few of them active at each time. When completed those, toggle some more active, and move to them.

The bad ones are the ones added by you just hearing some conversations. For the others, if you suspect the NPC may give you a quest (sometimes you can see that in their dialog options) just exit out of the conversation. That is how I keep it down.

Yeah, I do this sometimes. I hate forgetting the story to a quest

This- pretty crucial if you want to get use from your HUD flags. Setting a custom destination marker can also help with that.
As for just having a lot of different things to do and "loosing track" - don't sweat it. None of the quests are time sensitive, despite what the NPC dialog may say. So if you end up finishing a dozen part way, then starting another dozen... and working on them before you get back to any of the others, no problem.

I ran into this same problem and at one point kind put the bigger quests on hold to mop up alot of the misc quests and clear up the journal. This had the side effect of allowing me to level up pretty well, experience all the nooks and crannies of the game, and still have the bigger main & side quests to do once my character is badass. I even had to up the difficulty around level 40 and now the enemies are not one-shots and game is hard again! Loving it.

FWIW I keep them all active, every single one. I find it helps when I am traveling around and looking at the map- it is like "oh- I can do 5 things while I am here!" Otherwise I would keep forgetting quests and wasting my time going to towns over and over.

I keep them all active (except the ones I don't want to do) and just run around and hit all the markers.

One of the few things I dislike is all the darn quests. It seems to be the norm with RPG's these days to jam pack as many dumb quests as they can into a game. I would prefer quality over quantity and have the whole world to wander and explore without fear of breaking some dumb quest.

Make a toon to just DO that. Don't worry about any of the quests.... I have a couple of toons I just explore on - head south from Helgen, poke around, die some, clean out keeps, watchtowers some, kill a lot of wolves, bears....

There needs to be a journal organizer that separates Misc quests by cities/regions.

Thanks guys. I usually just keep one quest open at a time, do that one and move on. I think I will keep a few going at the same time and they might go down a bit quicker.
Backing out of a conversation with an NPC is a good idea too, I can always speak to them again when I'm in town.

I don't think I will ever complete it, I've already put in 100+ hours and I'm only at level 28

But you could think of changing that mindset if, at the same time, the ridiculous amount of active quests bothers you. I mostly don't get many quests at once at all. (Mostly though because I roleplay a character who usually is pretty strict at what he does at all; not so much to do in the game for one character like this.) Try making mental notes instead of keeping all the quests active. Think, "what should I do when I visit Solitude next" and the like. And even if you forget something... well, does it really matter? You can surely go back to that city (and fast in IRL time too, with fast travel) and finish your remaining jobs there later.

I sometimes rush through an Elder Scrolls game for apparently no reason as well. Lately I've tried to settle down, explain to myself that everything in the game waits for me and I have no real hurry anywhere. There's actually more gaming time and less stress to be achieved if you play slowly and non-systematically!

I use the misc quests to take a break from the biggies. Its a chance to explore but get something done at the same time. Great way to kill an hour or so.

It doesn't bother me personally, and I like my mindset. My journal is my character writing that stuff down, and me checking the quests when I see them is me looking over the notes. When there are 50 quests running I will hardly remember that: I should change the books in this shop while I am here. If I don't then I will just have to travel all the way back and then out again for 1 insignificant thing. I seem to be the minority in this issue. eh-