My boss has been closed for submissions for over six months. People still send her queries. If it were up to me (because I'm the strict one), every unsolicited query (my boss sometimes asks authors she meets at conferences to email her stuff) that came in during the closure would get an automatic rejection. However, my boss is a nice person, so every email gets read and evaluated. My current assignment is to help my boss get caught up with her backlog, which means reading every query, partial, or full that's been sitting around, waiting. I've been trying to make this a priority because some of these authors have been waiting for months, which, good God, I commend them on their patience. My head would have exploded from the anticipation by now.
If you've been caught in a submission limbo hell, my sympathies, man. Check the agent's webpage for any language about sending follow-up emails. My boss doesn't specifically say anything, but she makes it clear that it'll take about two months for a response. Personally speaking, as in this is my opinion and my opinion alone, I've made it a priority to read manuscripts where the author sent a polite, professional, follow-up email after three months have lapsed. The follow-up tells me the author has been keeping track of the queries they've sent out, that they are actively engaged in getting their book published, and that my boss is still someone that they are interested in hearing from. In today's market, authors need to do their part in marketing their books, whether through Twitter, Facebook, or a blog. So if you're on the ball enough to know when to send a follow-up, you can probably handle a blog book giveaway. However, multiple emails in a relatively short time frame sends up a red flag. Patience is your best friend during the submission process.
If you've gained representation from another agency, dude, you rock! Our team missed out so you should send a polite, professional, email that informs us that you are withdrawing your manuscript because you've been contracted elsewhere. This helps us because then we don't devote time to reading your totally awesome, but unavailable, submission and we'll just have to buy the book like anyone else if/when it get published.
If your patience has completely run out and you've decided to self-publish because you want to share your book with the world, please send the agent a polite, professional, email informing them of this. Janet Reid and Rachelle Gardner (professional literary agents that I don't know) share their opinions on the subject quite articulately. My boss has a similar policy. From my personal experience, I've gotten burned twice where I spent time reading the manuscripts and really liking them, only to find out later they've already been self-pubbed. It's frustrating as hell, especially for this one book that I was loving and mentally plotting different ways to make it shine like a frickin' diamond, and it was all for nothing. Please, won't you think of the interns? Email.