60GB is better, because:
1). It supports PS2 games (US version is the best - it has Emotion Engine chip to deal with that issue, euro version is good too, but it run old games on software emulation). 40GB version doesn't support PS2 games at all. Only PS1 games can be played.
2). It has 4 USBs (40GB has only 2).
3). It has memory slots (40GB doesn't have that)
Both versions have wi-fi.

http://en.wikipedia.org/wiki/PlayStation_3