I wasn't really sure whether this should go in Feature Suggestions or here, as the topic is a little about both...
Strafing with the mouse - it's impossible to get it to go any faster than walking speed. I know this one's a bug, as in the original Doom, you could use the mouse to strafe all the way up to running speed.
AutoRun stuff - even with it turned off, using , and . to strafe will cause you to strafe at running speed. I imagine that's a bug too, since it doesn't seem to make any sense.
Also, when AutoRun is on, shouldn't holding Shift make you walk? Since AutoRun wasn't in the original Doom, I guess this one would be a feature suggestion (although it could be a bug).
I think that about covers it. <!-- s:) --><img src="{SMILIES_PATH}/icon_smile.gif" alt=":)" title="Smile" /><!-- s:) -->