What you need is a boost regulator (finding one in the right amperage and input voltage will be fun, trust me). You trade a higher current drain from the battery for a higher and regulated output voltage. Don't use this without some kind of cell protection, as Bad Things will happen. But it will let you get 5V off a single cell, which will let you use one big cell rather than two small ones (more energy density) or a cell-phone flat-pack (more flexibility in form factor in general).I woould also like to make a 5v rechargeable but that would reuire balancing the batteries. Once I perfect the single battery I will start researching that.
Been playing around with some ideas using a gumstick battery, that being as close as flatpacks come to a standard size that's useful for our purposes (roughly the same as an old-style 5-piece pack of Wrigley's, hence the name).
--Dave