I agree with corkyg that rubber ear syringes are useful and cheap (and easily replaceable if lost). I always have a microfiber cloth - I think a t-shirt is a bad idea since it will usually contain at least a bit of sweat which I'm sure is not good for coatings. I also have a small bottle of lens cleaner which I sometimes need. I don't carry an extra battery only because I've found I don't need one. I've never run down my D70 all the way even while shooting > 500 shots/day. If I ever go backpacking I'll probably add a few batteries. I have an extra 2GB CF card but also carry a Hyperdrive HD80 with an 80GB drive to hold backups as well as running out of space. I generally copy any card I pull out of my camera over to it even if I don't need both of my CF cards. In terms of filters, I have a ND Grad filter, CP, and UV filter (which I use only in more "dangerous" situations). For my SB-600 flash, I carry a small bouncer if I'm outside and need to use it along with a Better Beamer for longer flash photography (for wildlife). Getting a diffuser is on my list of things to do. No colored gels yet for me - I just don't use flash that much and when I do use it, it's typically for wildlife where I need all the power I can get.
I typically don't use tripods. When I do travel or hike, I bring a Velbon 343e with me. If I'll be near my car most of the time, I have Bogen 3001 legs with a 3-way head, but that's rarely used due to weight. At some point I'll get a carbon fiber tripod but they're too expensive at the moment. I don't use gray cards or do manual WB since I don't think I need them and auto WB works great 99% of the time. I do have a rain cover for my camera. They're a bit annoying, but I've found it to be worth it. I also have reusable silica gel packs for travel in humid countries without A/C. Also, if you don't like your current neck strap for your camera, the Pacsafe strap is very nice and is also theft resistant, though I got it mostly for its good design.
I'll also mention that I think bags are a very important accessory. I personally have two now - an older Lowepro Rover Plus AW that I use for hiking and an new Lowepro Fastpack 250 which is great for traveling and cities. Depending on your needs I find spending money on a bag to be extremely important since that will determine how easy it is for you to use your camera.
As for the TSA rule, I highly doubt you can board with 3 bags (well, they might not stop you, but officially the rule is 2 for all airlines I know of). This will be especially true now that people are carrying on more and more.