Larry J makes a good point about where to place the capo. It's worth adding that you then only need enough tension to pull the strings taut over the fret, not all the way to the fretboard.
However, there is another problem that a lot of people run into when using a capo: their guitar isn't really "in tune" to begin with and using a capo just makes it worse. Tuning a guitar is a series of compromises. Unfortunately, most electronic tuners don't make the proper compromises, resulting in a guitar that is not really very close to being in tune.
Many years ago, I read an interview in Guitar Player magazine with a guitar tech (I think he was touring with Eric Clapton at the time). He mentioned that he used an electronic tuner to get close, then fine tuned by ear. I sat down with my guitar and figured out some tweaks that made a big difference. I found that if I tuned as follows, my guitar played a lot more in tune:
E: Dead on
B: Slightly flat
G: Dead on
D: Dead on
A: Slightly flat
E: A bit more flat
I now use a Peterson virtual strobe tuner, which has a sweetened (tempered for guitar) mode and find I don't have to tweak it at all after using the tuner. And I can then capo without having to retune (I capo a lot, as high as the 7th fret).
My recommendation would be to make sure you're getting your guitar as well tuned as possible first, then place the capo right next to the fret using the minimum tension possible to get clear, ringing tones.
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