Well I tihnk the tile says most of it, This is the CSS file for my site.

#top {
 background:#444;
 color:#fff;
 width:840px;
 padding:5px;
 margin-left:auto;
 margin-right:auto;
 margin-top:20px;
 margin-bottom:0px;
 text-align:left;
}
#top_nav {
 background:#444;
 width:850px;
 margin-left:auto;
 margin-right:auto;
 margin-top:0px;
 margin-bottom:10px;
 text-align:left;
}
#top_nav ul {
 list-style:none;
 margin:0;
 padding:0;
}
#top_nav li {
 float:left;
 border:1px #fff solid;
 height:20px;
 text-align:center;
}
#top_nav li:hover {
 float:left;
 background:#fff;
 height:20px;
 border:1px #fff solid;
 text-align:center;
}
#top_nav a {
 padding-top:2px;
 display:block;
 width:80px;
 height:25px;
 color:#fff;
 text-decoration:none;
}
#top_nav a:hover {
 padding-top:2px;
 color:#000;
 width:80px;
 height:25px;
 text-decoration:none;
}

The site looks great in FF, Opera, Chrome, and Safari, BUT when I look at it in IE the the menu (#top_nav) is longer than the header (#top). I don't know why this is, but if somebody could help me and tell me how I could fix it I would be thankful.

What VERSION of IE??
Prior to the patch that fixed IE6's busted box model, you might be right about padding being treated differently. However, since then, IE's box model is in line with the W3C specs - same as the other, better browsers.

The IE version I'm using is IE7. Any ideas on how I could fix it? The only way I could think of is using a conditional comment, but I'd rather just have one style sheet

Are you using reset css file?

Is unbelivable but is true also IE7 can cause serious problem and not showing same layout as other browser...

exactly I can tell why any single bug!! ...

IE is just the worst browser ever I suggest you to make a css file for it just for IE7 only where you correct the padding the margin all the discrepancies untill look same as other browser....

my 2 cents

Can you show us the screenshot? Cannot imagine what went wrong now... :P

The difference would be coming with using measurement in 'px'.

padding: 15px; in firefox wont be the same as in Explorer.

I always use "em" for padding now, gives me significantly less problems.

1em = 16px 0.5em = 8px etc. You can use it to 3 decimal places, but not necessary if you are consistantly using em for padding and margins.

padding: 15px; in firefox wont be the same as in Explorer.

Says who?? A px is a px is a px, doesn't matter WHAT browser you're using! You might have some very fractional differences due to IE rounding errors, but it will not turn 15px into 18 or 20, or anything else.

The only way I could think of is using a conditional comment, but I'd rather just have one style sheet

Good luck with that. With the many bugs in IE versions, even 8, that's nearly impossible.