As an assistant (AKA: Literary agent in training), for a well-respected literary agency in San Francisco, I read a lot of queries.
And by a lot -- I mean hundreds. A week.
One thing I like to remind people is: submission guidelines are there for your benefit. How do they benefit you?
It will get your work read, which is the entire point -- right?
An agent is more inclined to respond (generally, no response means "no, thanks," but in my case, I am much more likely to respond with some feedback if I felt the presentation took effort) if you properly prepare your work. These guidelines help agents get through queries quicker and more efficiently.
If you are unsure what the guidelines are, it is perfectly acceptable to email the agent to clarify.
How to gain brownie points with an agent:
* When sending an SASE -- make it self-sealing.
* Sending work that has been reviewed by several people, other than yourself, for simple errors.
How to sabotage yourself:
* When mailing your full manuscript, upon request only, do not send in READY POST MAILERS. They tear easily and are a HUGE mess.
* Don't follow the guidelines. If you can't follow simple rules for submission, then clearly you aren't going to follow the rules of your contract, etc. You want to show that you're willing to work with them -- not do you own thing.