Obviously, the big stand out figure is the marked increase in iPhone sales in 2009 over previous years.

But what stood out to me was the fact that:

Net sales were $36.5 billion for the fiscal year, $5.7 billion in net income, bringing Apple’s cash on hand to $34 billion.

For as long as I can remember, Apple’s largely been (not always but most of the time) good at keeping a nice chunk of cash on hand during the latest upswing (since Steve Jobs returned to Apple). No news there. But $34 billion?

But, after digging into the 10-K, something I haven’t done in a couple years, I’m not sure that’s such a realistic number. Actually, if you look carefully enough, you might find a reason to be worried a bit.

The $34 billion is actually the “Total cash, cash equivalents and marketable securities” part of the financial show of which cash is only $1.139 billion. The rest are various securities in various quantities. And, while SOME of the securities are indeed short term and could be used if needed within a fiscal year, the interesting thing to note is that there’s actually been a rather noticeable shift between 2009 and 2008′s numbers.

Where 2008 showed $368 million in cash on the books (yikes!), 2009 had the $1.139 billion I mentioned. Great, more cash is good in a way. It means if something goes wrong you’ve got something you could use to cover your ass. Granted, Apple is a big enough company that I’m sure it can always defer something until it liquidates other assets.

What’s more interesting is the shift from a heavier cash equivalent and short-term securities slant to a long-term securities bias. It’s not ridiculously dramatic but it’s noticeable. Cash equivalents went from $11 billion to $4, short-term securities went from $10 billion to $18, and long-term securities went from $2 billion to $10. Of the “$34 billion” in cash, only about 12% of that is true short term securities they could off-load (most likely) today. The rest is up closer to a year or more.

You can also see this shift on the cash flow statement where the purchase of marketable securities was more than double 2008′s at about $47 billion. Meanwhile, they received (through maturity of certain securities) roughly $20 billion which is close to but less than double 2008′s $12 billion. Actual proceeds from sales was up over 100% from $4.4 billion in 2008 to $10.8 billion in 2009. Nothing else on the cash flow statement moves around that much from year to year.

What does this mean? Probably not a whole lot. It looks like someone’s playing around with securities. I guess the thing that worries me most is that a lot of those securities are “US Agency securities” and Corporate securities (stocks and bonds). If you add it up, of the $34 billion in “cash”, upwards of $20 billion is in these securities which generally represent non-guaranteed securities. US Treasury securities usually are US government issued (and backed) bonds, t-bills, etc. Less speculative (depending on how you look at our government’s budget today, though) but also weaker in terms of returns.

So what’s wrong with this picture? Well, not that it will necessarily happen but $20 billion in “possibly” secured investments (US Agency securities aren’t all guaranteed) is a bit scary in an age where everyone’s getting bailed out and major companies no one thought could fold or file for bankruptcy actually did.

And, the other side of the coin is this: if you’ve got $20 billion you can spend on speculating in securities investments (which of course can add to the bottom line…no problem with that), why wouldn’t you try to put more of that back in your company (R&D is something like $1.3 billion…for a company that innovates and books $36 billion in revenue with 30% gross margins, that’s a bit cheap) or hand it out to your loyal shareholders (damn my father for not giving me money for Apple stock back in the late 1980s)?

I’m not saying investment activity like this is unexpected but I do wonder why more funds aren’t being dished out to parts of the company that could improve its growth and outlook even more so? Why not establish and donate some of those funds to a couple of non-profits: one to help bolster the education system in California (which can send you back top graduates while also showing how much you care about students–one of your best markets) and another to fund start-ups with interesting technologies or innovations?

Remember, the multi-touch interface came from research done OUTSIDE of Apple. Why wouldn’t you corner the market on computer repair nanites or holographic monitors? Or better yet, creating a better battery for my brand new iPod Shuffle which can’t hold a charge longer than a few hours while OFF?

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