The problem with things like width:95%;
is that they don't look right in wide flexible layouts (because 5% can then be like 30 pixels).
The following solutions works very well for me (tested in Firefox, IE 9, Safari):
<table style="background-color: blue; width: 100%;" cellpadding="0" cellspacing="0">
<tr>
<td style="background-color: red; padding: 3px;">
<div style="margin-right: 3px;">
<div style="padding-right: 3px;">
<input type="text" style="width:100%;">
</div>
</div>
</td>
<td style="background-color: purple; padding: 3px;">
<div style="margin-right: 3px;">
<div style="padding-right: 3px;">
<input type="text" style="width:100%;">
</div>
</div>
</td>
<td style="background-color: green; padding: 3px;">
<div style="margin-right: 3px;">
<div style="padding-right: 3px;">
<input type="text" style="width:100%;">
</div>
</div>
</td>
</tr>
</table>
(added the colors to make it easier to notice the correct padding)
The trick is to wrap the input with two divs, the outer has a 3px margin (which makes it 3px smaller than the td), the inner has a 3px padding. This makes the input 6px smaller than the td, which is what you wanted to begin with.
I am not sure about the mechanics of this, but it works.
In this simple example, it also works with just a single div with right margin 6. However, in the case of my web application, only the above solution works.
<table style="background-color: blue; width: 100%;" cellpadding="0" cellspacing="0">
<tr>
<td style="background-color: red; padding: 3px;">
<div style="margin-right: 6px;">
<input type="text" style="width:100%;">
</div>
</td>
<td style="background-color: purple; padding: 3px;">
<div style="margin-right: 6px;">
<input type="text" style="width:100%;">
</div>
</td>
<td style="background-color: green; padding: 3px;">
<div style="margin-right: 6px;">
<input type="text" style="width:100%;">
</div>
</td>
</tr>
</table>