It's always a case by case basis and I'm not a professional analyst, but I could come up with a few (flimsy) reasons.

Basically boils down to odds and the change in growth rate. Just because a company is consistently, wildly profitable does not mean they should have a high P/E ratio. P/E is often much more influenced by the growth rate for earnings. With Yahoo and eBay, investors are saying that these companies are more likely to grow very quickly than Apple and Google, which makes perfect sense since those two giants will most likely grow between some range. Investors must believe Yahoo is either be a huge hit or miss and eBay must have some reasons for people to believe they can juice their growth rate higher quickly, perhaps based on their acquisitions, room to expand their fees, acquiring new customers etc.

*Edit: Added note on Yahoo, its assets (as the Asian comment below reminded me to add) could very well be worth more than its current valuation. This article explains how: http://techcrunch.com/2011/06/24/yahoo-shareholder-bartz/

Asian assets are a very large part of the 'P'

Yahoo! is only a minority shareholder in Yahoo! Japan, with SoftBank owning 40+% of the shares.

Yahoo! owns over 40% of Alibaba which is a multibillion dollar company. I have seen valuations over 30B, but these are rough estimates since it is not public.

Market cap of $18, assets on balance sheet of $15 bn... some portion of that value may be breakup / liquidation value. In theory, a company is worth the greater of its future earnings (hence P/E) or it's liquidation value. (This assumes they're rational enough to break it up if that value is greater.)

So in theory, Yahoo's earnings could go to zero, and it would still be worth $15bn because you could liquidate the assets... and the P/E would rise towards infinity.

Well, non-cash Assets are often valued way above the firesale price they'd fetch in a rapid liquidation. The $4B in goodwill is not easy to extract.

True, but they have significant investments outside of their own business that would likely hold value, plus the assets on balance sheet don't include any patents, etc. that they own and might have standalone value. I'm just saying that's why the P/E will tend to float higher than you'd expect on the comps alone when you get down to certain market caps.

Price to sales is a better number for Yahoo, as it is for any company that is either losing money or on the edge of doing so. But with P/S you have to compare companies to very similar competitors like Google and cannot compare to hardware manufacturers like Apple or resellers like Amazon.

Apple and Google are probably cheap relative to Yahoo and EBay.

I'm not sure that this is true. Yahoo's earnings are around 1.2 B, and Market Cap is around 20 Billion, whereas Apple's Earnings are around 20 Billion, and their market cap is around 400 Billion. Very similar, unless my numbers are outdated.

I guess so. Overhead is much lower for the SOs though, so I can see why they are in such good standing. eBay, on the other hand...?