I love my X40, but I do like my X60s a lot as well. They both have advantages.
X40
Advantages:
- Sightly smaller
- Full size Ctrl + alt keys on both sides as it lacks a Windows key
- Runs cooler than my X60s
- Slightly brighter display I find (Could be that my X60s was abused, not sure)
- A cosmetic thing, but the Red stripes on the mouse buttons (I like this)
- Cheaper to obtain
Disadvantages:
- 1.8" hdd (Performance killer, also limits size)
- Only 1.5GB Ram
- Windows XP is the newest OS I feel comfortable running on it
- Orange thinklight rather than the white light (Personal preference though)
X60s
Advantages:
- Faster processor
- SATA HDD
- mPCIe
- Newer styled buttons on keyboard (Lacks the red stripe though

)
- Has a dedicated Windows key + menu key
Disadvantages:
- Runs hot
- More costly because it's newer
- Limited to 3GB, but not really a big deal IMO
- Smaller ctrl + alt keys, harder to press sometimes.
I can't really think of any other advantages/disadvantages for either computer. I like them both.