A couple rules of thumb:

1. Try to tune downward whenever possible. Too much stress on the strings is not good for the guitar or the strings (or you, for that matter). If you do tune up to a note, try not to go higher than three half steps.
2. Use a capo. It's much easier on your guitar to tune to Open D and then put a capo on the second fret to get your Open E. Ditto with Open G to get Open A. If you listen to the Rolling Stones' Happy, you'll find it's in the key of B. Richards uses Open G tuning with a capo on the fourth fret.

Remember that nothing is set in stone. But having said that, I will add that it is preferable to have your two lowest notes be the root and the fifth of your chord.

You can get a reference pitch by using another guitar that is in tune, a piano, a tuning fork, an electronic tuner or your computer. The easiest way to retune your guitar is to use a keyboard (which is hopefully in tune to start with). Most electronic tuners will allow you to tune to specific notes as well.

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