Does anyone know of good resources to get started with working with bitcoin? Mostly involving transactions, eg: creating and storing wallets and moving coins from one wallet to another, etc. This will probably be server software like for a website. I'm new to this and would appreciate some direction. Thanks.
There is a testnet for this sort of thing so you don't lose any money playing around. See https://en.bitcoin.it/wiki/Testnet and http://sourceforge.net/projects/bitcoin/files/Bitcoin/testnet-in-a-box/
After that you'll have to decide what approach you want to take. Are you integrating bitcoin into a larger project, or do you want to play with the internals? You can run a live bitcoind node and interact with the network through RPC commands if you just want to integrate it as a payment method. See https://en.bitcoin.it/wiki/API_reference_(JSON-RPC) for whats available.
This won't get you into the nitty gritty of the protocol though. For that the best place to go would be bitcoinj. https://code.google.com/p/bitcoinj/
I would also suggest looking into Armory's software if the purpose is interacting with wallets in an online environment.