mr Bob is right about keeping things simple! I’ll try and answer some points for you.
* We’ll be working with a linear workflow. Is there a “correct” way to do this? I always just use mia_exposure_simple.
There’s no one perfect way to do it (in Maya), unfortunately. The different methods are annoying in different ways. If you are using the mia_exposure_simple you are halfway there, but you need to be correcting your textures and colour swatches first in preparation for the lens shader. Everything needs to be ‘linear’ the whole way through the process. Textures painted in Photoshop or used from photo reference are not linear unless you tell them to be. You can either do this by saving them as an EXR file, or in Maya use the Gamma utility node to linearize them using gamma values of 0.454. That takes the default 2.2 gamma out of them. You also need to do this for any colour swatches or procedural textures that are assigned to shader properties that show up as colour in your render, ie a diffuse/colour swatch, specular colour, transparency colour etc. Even the colour swatch for your lights. Otherwise the lens shader will make things look pale and too bright. There are some scripts to help you manage this process such as the one found here:
http://forums.cgsociety.org/showthread.php?f=87&t=899672
Sorry if I raced through that explanation but you may already know all of that, or I can answer more questions later. 
There are other options out there too such as the DeeX shaders which have gamma correction built in, but they use their own pass system which is different to Maya’s (though you may like that).
* Regarding Final Gather and Global Illumination. How is the best way to handle this for a production? I’ve never even worked on an animated scene before (mine are all stills). I’d like to be able to do things efficiently.
Well it will really depend on a number of things, such as the complexity of the scenes and lighting, how much flexibility you want in the compositing stage, how long the animation is versus how big your renderfarm is etc. Also how much technical understanding your artists will have or if you’ll have someone (maybe a lighter) designated the rendering troubleshooter if need be. Each new version of Maya comes with a newer mental ray version and better features for managing indirect lighting, so hopefully your school is nice and upgraded Maya for you, but you’ll still get by with 2010 of course. 
Final Gather by itself will likely be much easier to handle than FG + GI together, so consider that option or even do some tests if you have time to see how you feel with the workflow.
* Render passes. The best way that I’ve found to do them is create separate files for the diffuse, specular, shadow passes, etc, just because I don’t like the way Maya handles them. Are there any free resources compatible with Maya and Mental Ray that lets me handle render passes more efficiently?
Having them as separate files is ok if you only want a couple of passes, but if you end up with 30 shots in your animation with 10 passes each… that’s 300 separate files and if you make changes to a shot you need to recreate or update all 10 files for that shot! Way too many opportunities for things to get messed up! Maya’s passes system is pretty crazy I know, but if you use the good parts of it without committing to it entirely it can work out well. Don’t forget that ‘Render Layers’ is a separate feature to ‘Render Passes’ even though they do go together. Quite a bit can be done with ‘Render Layers’ on it’s own. Almost the same as having separate files, but it’s all contained together and maintains connections to things so it’s easier to update with changes. There’s a big PDF on the distinction between Render Passes VS Render Layers… I’ll see if I can find it… here:
http://usa.autodesk.com/maya/white-papers/
On the right! Render Pass Concepts & Techniques. Things like ‘Contribution Maps’ can be really useful and we used them a lot (as well as the whole system) doing high end car commercials that need a lot of passes. Of course, you need to evaluate how complex and flexible you need things to be. Don’t go too crazy and feel like you should use all the power available when it’s not really that important for your animation!
* Outdoor scenes. People go bananas over physical sun and sky. I do outdoor scenes the way that it teaches in Jeremy Birn’s book, Digital Lighting and Rendering with two directional lights. One for the sun, one for the sky light. Is there some reason I should be using sun and sky that I don’t know about? And are there any decent resources out there on how to use it effectively? The only semi helpful thing I’ve found on it is this: http://www.mentalimages.com/fileadm…_and_design.pdf
Well, there’s nothing wrong with doing anything if it gets you the result you want. :arteest: The physical sun & sky does have a number of benefits, mainly if you are aiming for a more (or totally) realistic lighting style for your animation. Here are a few:
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It has a high dynamic range. If you’re using a linear workflow, you’d probably like your lighting to be reasonably correct in terms of comparative intensity etc. The sun is, well, freaking epic-ly bright! Approximately a gazillian times brigther than a street light for example. This means you’ll get nice intense highlights on your surfaces, perfect for adding glows and blooms in post etc.
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It is the right colour temperature, and adjusting the time of day etc changes the colour and intensity accordingly.
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There’s an actual sun, for reflections.
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It has some atmospheric properties like haze etc.
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It works really well with the lens shaders and indirect illumination. In fact, if you do end up using GI, the sun & sky knows the correct photon intensity and has optimisations built into it. Photons from a directional light are almost never a good idea. The photons would be coming from an infinitely large source and most of them would miss your scene entirely.
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It’s quick and easy to get a nice result, and still quite customizable in terms of style.
As for resources I can’t think of any off the top of my head I’m afraid.
