It's not for the faint of heart, given the inaccessible brick-ness of the Kindle and its long, nerve-racking reboot time, but you can jailbreak your device and install KUAL (app launcher) and KOReader.

http://www.mobileread.com/forums/showthread.php?t=203326

https://github.com/koreader/koreader

ePub and PDF support, text reflow/cropping/reformatting (great for papers!), plethora of options from contrast to margins, custom fonts, per-document style sheets, etc etc.

You can also install things like Gargoyle for interactive fiction on the go.

http://www.fabiszewski.net/kindle-gargoyle/

Just make sure to set up BackDoorLock so that Amazon can't force an OTA update on you.

http://www.mobileread.com/forums/showthread.php?t=205666

You might also want the Rescue Pack in case things go wrong. It boots you into diagnostics mode if you start your Kindle with a USB cable plugged in..

http://www.mobileread.com/forums/showthread.php?t=195670

(how to exit diags mode) http://wiki.mobileread.com/wiki/Kindle_Touch_Hacking#Exiting...

See the FGA thread and MobileRead's "Kindle Developer's Corner" for more info.

http://www.mobileread.com/forums/showthread.php?t=237083

http://www.mobileread.com/forums/forumdisplay.php?f=150