It’s a particularly good time to ask which is a better investment. Both companies are trading at or near 52-week highs – Apple is at a high of more than $120 per share, while Microsoft is just shy of its January 25 peak of $31.48 per share. (Add up all the shares, and Microsoft is still worth three times as much as Apple, according to the public markets.)

But if we’re pondering which stock to buy, the important thing isn’t which is worth more now, it’s which is going to have healthier profits in the future. Generally speaking, that’s how stocks are valued – when you buy a stock, you’re really buying the right to share in a company’s future profits.

So which stock is better? I’m a technology and business journalist not a stock adviser, so I’m not going to tell anyone to buy one over the other. But here are a couple of issues that come to mind as I wonder which company is poised to do better in the next few quarters:

AN IPHONE POP FOR APPLE. There’s pretty much one reason to buy Apple right now: the iPhone. If you believe the company’s device, due to ship next month, will be the hit product that changes the cell phone world, that’s the biggest reason to buy Apple stock. No other factor, including Mac sales or OS X Leopard, has as much potential to move Apple’s stock.

There are several reasons to believe the iPhone hype. AT&T, the phone’s exclusive carrier in the U.S., has said that 1 million people have asked to be notified when the phone becomes available. Analyst surveys show that the legion of iPod buyers are interested in the phone. And the broader public already believes the iPhone is the most innovative wireless product around – even though it isn’t, technically, around yet.

But there are potential iPhone pitfalls as well. Because Steve Jobs’s baby is arguably the most hyped technology product in modern history, there are likely to be supply shortages and scams. I expect that people who aren’t even AT&T customers will try to buy out the available inventory of iPhones in order to mark them up and resell them. If it’s too much of a hassle to get an iPhone, phone shoppers will grab something else instead.

A REVIVAL FOR MICROSOFT. With all the talk about how cool Apple is compared to Microsoft, it’s easy to forget that the software giant managed $4.9 billion in profit last quarter alone – more than Apple earned in the previous four. And Microsoft’s profitability is pretty reliable; it’s not reliant on one or two hit product categories, so it’s not as vulnerable to changing fashion or consumer sentiment. Plus, despite flops like the Zune, Microsoft has a decent track record for eventually figuring out consumer markets. Case in point: Microsoft’s Xbox 360 is considered on par with Sony’s (SNE) Playstation 3, a testament to Microsoft’s ability to break into important markets. And Microsoft’s Windows Mobile software for phones has secured a place in the next-generation mobile universe; even former arch-rival Palm (PALM) now makes a Windows model.

The question is, what will it take to send Microsoft soaring? The answer is, maybe not much. The premium on Microsoft’s valuation right now is considerably lower than Apple’s, despite Microsoft’s high profitability and potential for near-term growth. The main thing that could get the stock going would be a price war for mid-range PCs – something that might be brewing, as Dell (DELL) prepares to move into Hewlett-Packard’s (HPQ) turf, selling desktop computers at Wal-Mart. If the rivalry heats up and includes laptops this holiday season, expect Bill Gates to be the main beneficiary; it gets paid for Windows Vista and Office no matter how much Wal-Mart discounts the PCs.

Bottom line: Apple has considerable upside potential with the iPhone (though you have to wonder how much of that is built into the stock price.) It’s not clear what Microsoft’s next big hit will be – but it also seems likely that there will be one eventually, and that Wall Street isn’t expecting it.