I need two have two "per-item" shipping options, with different base prices and per-item rates. Standard shipping, not usps/ups/fedex. It doesn't seem like there's a good way to do this. I've read about setting up multiple flat rates, but I don't believe that applies to this situation. Anyone have an idea?
Its a little unclear exactly what you want to do here, but as Marius says you need to create a carrier based extension for this one.
You can then get access inside the $request object to the items ($request->getAllItems()) and also get access to any attributes you set up on the products (see http://www.atwix.com/magento/custom-product-attribute-quote-order-item/).
Inchoo has a good tutorial on creating shipping carriers: http://inchoo.net/magento/custom-shipping-method-in-magento/
You can create unlimited number of shipping options based on different conditions with the help of an advanced extension like Shipping Table Rates.
Create any number of shipping methods: multiple flat rates, multiple table rates, etc. Flat and percent rates. Combinations of address, weight, price and quantity to calculate shipping. Import rates and edit them manually.