I run two Pis in production at home:
One as a NAS with SMB, NFS and DLNA
The other as a seafile server
That's what is left when the server is up and running:
pi@raspifix ~ $ free
total used free shared buffers cached
Mem: 496592 430080 66512 0 112996 230412
-/+ buffers/cache: 86672 409920
Swap: 0 0 0
and
pi@seafile ~ $ free
total used free shared buffers cached
Mem: 496592 484912 11680 0 13292 346204
-/+ buffers/cache: 125416 371176
Swap: 102396 8 102388
Both work fine and perform well. As you can see the seafile server has approx 371MB free (caching aside), which is more than the 44MB you reported in your case.
Don't worry about the free memory left. Linux is able to handle the free memory very efficient. Unless you have a serious amount of memory swapped you should be fine.