Absolutely. By cleanly I mean no noticeable side effect after uninstalling. Sorry if I caused confusion by not inserting a big gap between the second and third sentence, BTW.

Software hacks are pretty well covered but since you mention the device itself as well here are some great hardware mods I have done and can give great reports.

Fix the USB port, this is pretty much mandatory, I only use my USB port for host mode but I still like to have it available for that and when charging from a battery pod or in/on bike/car/airplane without an inductive charge base.
http://talk.maemo.org/showthread.php?t=37107

Installing Touchstone inductive charging also requires some skill but as long as you are doing the required USB reinforcement what is soldering down two more wires. Never worry about your phone falling and breaking the USB port again. If I could figure out the USB charging BME mode and could wire it to the USB pads rather than using a charge controller to the battery pins it would even show up charging in the battery status. Requires the Mugen cover below.
http://talk.maemo.org/showthread.php?t=56950

Lastly the easiest bit also possibly the most explody still requires soldering, the double Scud super battery. My wifes N900 lasts a day with heavy phone use, mine lasts two days easy, up two four if you reign back wifi, HSPDA, and phone. Uses a Mugen cover which leaves room for the inductive charging bits from a Palm Pre Touchstone set above.
http://talk.maemo.org/showthread.php?p=1355160

/home/user/.profile and .bashrc are empty
/root/.profile and .bashrc don't have anything suspicions
Thanks!

EDIT: Speedpatch adds stuff in /dev/cgroup/ (I have no /dev/cgroup now that I've uninstalled Speedpatch)

I discovered this thread looking for some gen on the FlopSwappolube combination, and thought it was missing something.

...but not entirely. If you use the N900's calendar capability, you'd be insane not to install Qalendar. It allows you to use all the basic funtionality (set entries attimes not in multiples of 5 min, set arbritary alarm times for events, set complex event repetition rules... just follow the previous link to the wiki to find them all) that have always existed under the Maemo5 hood but which the standard calendar frontend doesn't exploit.

If you use an N900 to organise your life and haven't installed Qalendar, go and do it right now.