How does your mom check it? Does she enter your room or check your computer?

Tell her to piss off.

could watch it on your phone if your phone supports video?
i am a big android fan tbh so u can guess i has one, and when i was really bored in college at dinners i used to take elfen lied- head off to the libary and watch it suppose it sounds sad but it was fun
also, try distract her, to buy 25mins here and there
a good thing i used to do bk before i had my own computer... and i was like 13 was wait up till everyone was in bed then watch wot ever... (that was more playing games n stuff but works the same)
also i guess you could wait till she watches tv? although im in england so im unsure of the rest of the world but i know lots of mums espically love soaps so really 5-8pm is a nice time to score a win also another thing u could try, find another show she dont mind you watching, open up your video player in 2 windows, one with elfen lied, one with the other show, keep the other show around mid-way in paused then watch EL in normal sized window (shame wont work in full screen unless ur mum is dumb which i doubt she is) then drag the EL window to the courner and watch, upon hearing her approach (stay alert) minimize fast to the other show (u could leave the other playin on mute aswell as its more effective) just rename the elfen lied file temporarily to somthing else so if she looks in ur taskbar she wont suspect...
worst comes to worst, put it on disc or find somwere to watch it online and go to ur friends house (or a public net cafe or libary)
there just some simple thoughts

Realize this is old and such. But you can also go to iphoneanime.net if you have an iPhone. Just a heads up for everyone here as well. It has a crap ton of anime there, and it's all free and easy to use.