This will be my next thing to save up for. Do you have any recommendations?
Miller is a personal favorite. I've also owned a couple Manfrotto tripods which were ok for the budget oriented. The other big names are Cartoni, Sachtler, and Vinten. I've used them, but with the bigger cameras so I can't attest to their offerings for smaller cameras.
Tripod systems can cost a small fortune, but you do get what you pay for. If you have the opportunity to try any out in person then I would try to do that. That can be difficult depending on where you live though.
What sorts of lenses should I be looking at?
This is really just a matter of preference. If you want to work with primes, then maybe look into building a set, but I'd also include a good zoom in there for any situation where you want to move between the range quickly. For zoom lenses, look into one that has a constant aperture. This makes the lens more expensive, but better for video use.
I will make do without the view finder and follow focus for now, but they will definitely be put on my wish list. ND Filter sounds like a must?
The ND filter is important for shooting outdoors or any bright situations, especially if your intent is to open up and get that shallow DOF. You can't just up your shutter speed like when you take stills (well you can, but you'll probably get unwanted results). You usually want to keep your shutter as close to the standard 180 degree shutter of a regular motion picture camera. This would be 1/60 if you're living in the NTSC world, 1/50 for the PAL people. So the ND filter(s) is what helps you accomplish this.
You can get individual ND filters in different strengths, or stack them (either on the lens or matte box). But I've found the fader ND filters work extremely well. This is a single fader that changes the amount of ND as you turn it. So you can cover a wide range of ND with just one filter.
I recommended buying the largest diameter one since you can just use cheap step down rings to fit your lenses, instead of the other way around of buying multiple ND filters for all of your lenses.
Do you know if the 60D does live output? And would it be hdmi or composite?
I'm not sure actually. I think it performs just like the t2i in this regard, which I think is an SD signal out through HDMI. I think only the 7D offers a live out that is near HD quality.
Follow focuses seem really expensive. Is the D|FOCUS any good?
A follow focus can be really expensive. I don't have much experience with them, but as with the tripods more often than not you get what your pay for. Zacuto and RedRock micro have sort of led the way with DSLR accessories up to this point. Redrocks products seem to sit in the middle of things price wise whereas Zacuto is insanely expensive. But everything I've seen from Zacuto has been solid, so if you have the money then their products are a can't miss. I've heard mixed reviews on the D focus. It's definitely aimed at the budget conscious so I don't know how dependable it would be. But at that price, it probably wouldn't hurt to try.
Videos on youtube of the 50mm f1.8 aren't too bad? What about the f1.4? it's more expensive, but would you recommend waiting on a prime until I can afford it?
The 50mm 1.8 has actually gotten some pretty good reviews. I think the biggest complaints I've heard are the build quality and poor design of the focus ring. I personally own the Zeiss 50mm 1.4, which I love. It's solid and has a much longer focus throw than most still lenses which is really beneficial for video use.
Also, keep in mind that a 50mm lens on the 60D will act more like a 80mm due to the APS-C sized sensor. So keep that in mind when looking at full frame lenses.
As for primes themselves, there's a huge market out there for used ones. I'd recommend building a kit out of used primes and just get yourself some cheap adapters (so you can use lenses with other mounts).
Here's a pretty good resource on lenses for DSLR use:
http://www.dvxuser.com/V6/forumdisplay.php?193-7D-Lens-Discussion
Also here's a good utility for searching used primes on ebay:
http://primes.decentattempt.com/list
Also with the filter's, what about a matte box with slots for filters?
This depends on how much filter use you think you would get into. A good matte box costs a lot of money. And as with everything else, you get what you pay for. If you think you'll get into some other types of filters and find the need to stack them, then a matte box is definitely the way to go since you'll likely be using different sized lenses. Otherwise, I think this would probably sit at the bottom of the list of important accessories.
I have photoshop, final cut studio & after effects.
Those should get you pretty far. The Canon utilities that come with the camera are pretty decent for bundled software. But if you feel the need to use something more robust, then Lightroom or Aperture would be good to look into.