Is there a comprehensive list of Gateways' IOUs and fees associated with using them? I am looking for information about the various IOUs issued by Ripple Gateways and what fees are associated with using them - namely fees to get the IOUs and transit fees.
There is no official list of Ripple Gateways because there is no such thing as an "official" gateway. Anyone can operate one without registering anywhere (other than as required by local laws in their jurisdiction). That hinders the creation of any kind of comprehensive list.

There are a few people that attempt to keep somewhat comprehensive lists but their list criteria for inclusion may differ or they may not hear of some new gateway for a while so I think they best you'll ever be able to do is to have a list of list of gateways.

Some places that attempt to list gateways:


DannyM's bitcointalk.org post, All Things Ripple (mostly up-to-date, lists all kind of niche gateways not listed elsewhere)
Ripple Gateway sub-forum (only indexes gateways discussed on the forums, does not claim to be exhaustive)
Ripple Federation has a Ripple Business Listing that includes a Gateways and Exchanges setion
The International Ripple Gateways Association's gateway list (they have some arbitrary requirements to join and don't actually police their members yet)


Of these, the only one I know that explicitly list the fees (or provides links to where the fees are listed) is the Ripple Gateway sub-forum topics.

The Ripple internal transfer rate for any issuer can be queried with the account_info API. The other gateway fees (for redemption, issuing, etc) are probably best determined by going to the fee page of the gateway's website.
Some other basic per-gateway information (such as issuing and hot wallet addresses) can be retrieved in a computer readable form from the sites's ripple.txt file, usually available from https://gateway.domain.name/ripple.txt.