I'd like to expand upon what Chris said. He said each mode has a feel or flavor to it, and that's absolutely correct.

This is a list of what I think about for each mode
Ionian=happy, plain
Dorian=jazzy
Phyrgian=dark, spanish
Lydian=spacey, out there
Mixolydian=blusey, celtic
Aeolian=lighter than phyrgian, but still dark
Locrian=really heavy, death metal-ish

Now, you can match chords to modes (i.e.-use ionian or lydian over a maj7, mixolydian over a 7, etc.), but sometimes it's hard to think like that while improvising. Check your chord progression. Em, D, C, D for example. The tonal center is 'E' (that's what chord it sounds good to end on). Now, just use any 'E' mode - whichever suits the sounds you're hearing in your head.

One might argue that the progression is in E Aeolian, but playing E Phyrgian over the progression sounds great and gives the piece a Spanish feel. If you play E Dorian, you get a brighter, jazzier sound.

You may want to make sure that if you're in a minor key (E Minor here) that you use a minor mode, just to be safe. However, that's no hard rule. For example, for one piece my band does in A major, I sometimes play A Dorian over it (I'm really aiming for a D Mixolydian sound, and D Mix. is what I'm thinking about, but translated into an A mode, since A is the tonal center, I get A Dorian).

To summarize all this garbage, try every mode (keeping the root the same as the root of the chord progression) over a progression (try G Ionion through G Locrian over a G, C, D) and see how each mode "feels". You'll soon catch on to the sound of each mode and the feel for when you should use them.

DISCLAIMER - Remember that this is only my OPINION on ONE way to treat modes. There are many other ways. Try TRY THEM ALL OUT and keep the one you like best. Or, if you're like me, trash everyone's ideas and find your own approach.