AAPL's PE is 20ish, and MSFT is 12ish.
Market Cap, P/E, EBIDTA, R, ROA, ROE, and EPS are fairly basic fundementals.
Also, take a look at balance sheets, cash flow, income statements, and Short Sales ratio.

Yes, AAPL has a higher market cap than MSFT, and AAPL is valued higher than MSFT relative to earnings.

I was super supporter of Apple products during 1994-2004.
Now, I am not an Apple fan at all. I do NOT own any apple products.




AAPL
VALUATION MEASURES

Market Cap (intraday)5: 222.12B
Enterprise Value (May 27, 2010)3: 198.97B
Trailing P/E (ttm, intraday): 20.69
Forward P/E (fye Sep 26, 2011)1: 15.83
PEG Ratio (5 yr expected): 1.12
Price/Sales (ttm): 4.36
Price/Book (mrq): 5.67
Enterprise Value/Revenue (ttm)3: 3.89
Enterprise Value/EBITDA (ttm)3: 12.59


FINANCIAL HIGHLIGHTS

Fiscal Year
Fiscal Year Ends: Sep 26
Most Recent Quarter (mrq): Mar 27, 2010


Profitability
Profit Margin (ttm): 21.15%
Operating Margin (ttm): 29.38%


Management Effectiveness
Return on Assets (ttm): 18.72%
Return on Equity (ttm): 33.97%


Income Statement
Revenue (ttm): 51.12B
Revenue Per Share (ttm): 56.76
Qtrly Revenue Growth (yoy): 48.60%
Gross Profit (ttm): 17.22B
EBITDA (ttm): 15.80B
Net Income Avl to Common (ttm): 10.81B
Diluted EPS (ttm): 11.80
Qtrly Earnings Growth (yoy): 89.80%


Balance Sheet
Total Cash (mrq): 23.16B
Total Cash Per Share (mrq): 25.45
Total Debt (mrq): 0.00
Total Debt/Equity (mrq): N/A
Current Ratio (mrq): 2.64
Book Value Per Share (mrq): 43.26


Cash Flow Statement
Operating Cash Flow (ttm): 13.49B
Levered Free Cash Flow (ttm): 6.91B

TRADING INFORMATION


Stock Price History
Beta: 1.52
52-Week Change3: 83.47%
S&P500 52-Week Change3: 19.58%
52-Week High (Apr 26, 2010)3: 272.46
52-Week Low (May 27, 2009)3: 130.91
50-Day Moving Average3: 251.86
200-Day Moving Average3: 219.57


Share Statistics
Avg Vol (3 month)3: 23,599,000
Avg Vol (10 day)3: 34,508,900
Shares Outstanding5: 909.94M
Float: 903.32M
% Held by Insiders1: 0.65%
% Held by Institutions1: 73.00%
Shares Short (as of May 14, 2010)3: 11.49M
Short Ratio (as of May 14, 2010)3: 0.40
Short % of Float (as of May 14, 2010)3: 1.30%
Shares Short (prior month)3: 11.50M



MSFT
VALUATION MEASURES

Market Cap (intraday)5: 219.18B
Enterprise Value (May 27, 2010)3: 188.00B
Trailing P/E (ttm, intraday): 12.96
Forward P/E (fye Jun 30, 2011)1: 10.83
PEG Ratio (5 yr expected): 1.49
Price/Sales (ttm): 3.84
Price/Book (mrq): 5.00
Enterprise Value/Revenue (ttm)3: 3.16
Enterprise Value/EBITDA (ttm)3: 7.45


FINANCIAL HIGHLIGHTS

Fiscal Year
Fiscal Year Ends: Jun 30
Most Recent Quarter (mrq): Mar 31, 2010


Profitability
Profit Margin (ttm): 29.03%
Operating Margin (ttm): 38.43%


Management Effectiveness
Return on Assets (ttm): 18.60%
Return on Equity (ttm): 41.83%


Income Statement
Revenue (ttm): 59.54B
Revenue Per Share (ttm): 6.72
Qtrly Revenue Growth (yoy): 6.30%
Gross Profit (ttm): 46.28B
EBITDA (ttm): 25.25B
Net Income Avl to Common (ttm): 17.29B
Diluted EPS (ttm): 1.93
Qtrly Earnings Growth (yoy): 34.60%


Balance Sheet
Total Cash (mrq): 37.19B
Total Cash Per Share (mrq): 4.24
Total Debt (mrq): 6.00B
Total Debt/Equity (mrq): N/A
Current Ratio (mrq): 2.06
Book Value Per Share (mrq): 5.22


Cash Flow Statement
Operating Cash Flow (ttm): 22.31B
Levered Free Cash Flow (ttm): 16.42B

TRADING INFORMATION


Stock Price History
Beta: 0.93
52-Week Change3: 24.24%
S&P500 52-Week Change3: 19.58%
52-Week High (Apr 23, 2010)3: 31.58
52-Week Low (May 28, 2009)3: 20.05
50-Day Moving Average3: 29.54
200-Day Moving Average3: 29.53


Share Statistics
Avg Vol (3 month)3: 63,265,200
Avg Vol (10 day)3: 89,340,100
Shares Outstanding5: 8.76B
Float: 7.71B
% Held by Insiders1: 12.25%
% Held by Institutions1: 64.90%
Shares Short (as of May 14, 2010)3: 66.00M
Short Ratio (as of May 14, 2010)3: 0.90
Short % of Float (as of May 14, 2010)3: 0.80%
Shares Short (prior month)3: 70.37M