Interestingly, my former employers had what I believe to be a more common system in Japan: they paid you more to live farther away from the office, by subsidizing your monthly train pass. (One could actually turn this into an untaxed wage increase by buying the 6 month pass at the standard discount, rather than six 1 month passes, and pocketing the 6th month's subsidy. Eventually HR realized this, cut the subsidy, and directed everyone to buy the 6 month pass. HR was surprised that this decision was unpopular.)

One of the reasons for subsidizing commute expenses in Japan is that they're typically both high relative to employee salaries and the benefits are not taxable as earned income, whereas giving equivalent sums of money for other purposes does make that money taxable. For example, my read of the relevant regulations suggests that paying somebody to live close to the office constitutes taxable income but subsidizing their commute is not.

In case it isn't obvious, I'm none of Japanese, a tax lawyer, a Japanese tax lawyer, or your Japanese tax lawyer, but the regs are fairly straightforward if interested parties want to look them up:

http://www.nta.go.jp/taxanswer/gensen/2508.htm

[Funny anecdote: My boss attempted to sell me once on moving next door to the office, on the grounds that this would save the company money on my train pass and let me continue working without that pesky hard stop at 30 minutes past midnight when the last train to Ogaki left. I think he was genuinely confused when I told him "I consider that less a bug and more a feature." The joke was on me, though, after crunch time happened and I had to buy hotel stays at my own expense after staying until 3 to 4 AM.]

I also received a bonus while working in London (I always thought it was called "London Waiting" [1], which seems like a more accurate a reflection of their train system).

I think it was £3000, which was a large amount back then.

[1] http://en.wikipedia.org/wiki/London_weighting