I'm having these same thoughts. Under the hood, there's no obvious place.
The intake swap that Grim mentions doesn't quite get you there cleanly on a 22R-E. The AFM is now in the old battery location and the air box location is where the battery goes. Reasoning behind this is to make the air path shorter for performance.
http://www.yotatech.com/f116/22re-intake-battery-swap-111508/
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I have a spare hanging under the bed, but the Roger Brown method could work with moving some things or in another location with small batteries. I'm also considering putting a battery in the bed of my truck. These sorts of things work OK, but it would be nice not to have to run a 2 AWG wire from the engine bay to the back. But OTOH, it does put the battery closer to the load. I figure the second battery in this case would be for accessories, so it wouldn't need to be a big battery.
Although a major part of the reason for me would be two batteries for a winch (that I also don't have) and back-up starting. I think under the hood is still my goal. I have a 22R-E and you probably have a 3VZ-FE, so I don't know how similar we really are, but I think if I move the ignition coil and ignitor I could squeeze in a battery there. Another option might be against the firewall on the passenger's side.
My last thought is to squeeze two smaller batteries in the same location as stock. There's some room around the battery as it is and it might be possible to shoehorn a pair of smaller Odyssey batteries in there. Maybe a pair of Odyssey 1200 or something. Not sure of their dimensions but they are smaller, right?
Anyway, no answers, I'm looking for a clean way to get a second battery in there, too. So I'll be watching.