I often find the middle of the manuscript is when things get murky.
The beginning is easy when you have that bright, fresh, shiny idea. You're pumping the words out, on an almost artificial high from the prospects of your new story.
And I don't know about you, but I like to know what the ending is before I start writing. Back in March, Maggie Stiefvater, wrote an excellent post about how to start a novel, and she mentions the importance of knowing the ending, but then she also says at the end of her post to ignore all her rules. I think they're valid rules, and I wouldn't ignore them. She's just being humble.
So, I'm not an expert, but these are some things that work for me when I'm stuck in the murky middle.
1. Close the laptop. Whip out some paper and pen and just start writing. It doesn't matter if you write a massive info dump or if you decide to spontaneously give your main character blue hair. In the midst of all the nonsensical words, you will find the answers that you seek to crawl out of the murky deep.
2. Talk it out with a critique partner. I find these conversations extremely helpful. Oh, you don't have a critique partner you say? Here are some links to help you find one: Maggie Stiefvaters Critique Partner Love Connection, and Agent Mary Kole's blog. Natalie Whipple also has some excellent posts about giving and receiving critiques. If you readers know of others critique partner resources please share in the comments section.
3. Sometimes, it's ok to stop writing for a few days. Just let the ideas stew in your head until you figure out where you story needs to go. This is probably my least favorite method. It has worked for me in the past, but the pesky side effect of this route is that sometimes that one or two days can turn into one or two weeks, and then you start to have a disconnect with your story, and then you're setting yourself up for the My story sucks or I don't know if I can write this anymore, etc...
Hope this helps!