PrBoom turns out to be a really bad test case. While it actually needs redundant joystick events to be spammed to work properly, most apps don't really appreciate that.

Version 0.0.3 brings better defaults for everything (except prboom). To use it with prboom, edit the main.cfg and reduce the maximum pitch and roll to around 8 and the thresholds to 0. Alternatively, edit and copy the file to prboom.cfg and pass that as the only parameter to the accelemymote binary. I.e.
/opt/maemo/usr/bin/accelemymote ~/.accelemymote/prboom.cfg

accelemymote (0.0.3) unstable; urgency=low

* Enabled threshold angle change between events (fixes many control issues).
* Better universal default settings (PrBoom has special needs).