The easiest way to avoid dissapointment is to do the checks that the moderators do.

First download test data from https://wpcom-themes.svn.automattic.com/demo/test-data.2011-01-17.xml
Import this into your theme and check that all the little things are fixed display correctly e.g.  Really long titles.

Once that is done check your compliance with W3C for html and css compliance.  You can do this with a neat little WordPress Plugin called Deblogger.

Next you will need to do checks to see if you have all the required standards for a theme.  The Theme-Check plugin will sort  this out for your.  After you run this you will find out if you have included all the required css and updated not depreciated calles in your PHP code.

Lastly get the Log Depreciated Notices plugin which logs the usage of deprecated files, functions, and function arguments, and identifies where the deprecated functionality is being used in your theme.

For the full guide on theme testing you should visit the Theme Development page in the WordPress codex to guide you further.

Notice: Undefined index: page in C:Users\Mysql folderrootwordpresswp-contentthemesbreathefunctions.php on line 298

The offending line of code is most likely this…

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if ( $_GET['page'] == basename(__FILE__) ) {

replace with this…

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if ( isset($_GET['page']) && $_GET['page'] == basename(__FILE__) ) {

Notice: Undefined index: std in C:UsersMysql folderrootwordpresswp-contentthemesbreatheindex.php on line 4

The code that is generally outlined and is the culprit for the errors is…

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<?php 
global $options;
foreach ($options as $value) {
    if (get_option( $value['id'] ) === FALSE) { $$value['id'] = $value['std']; } 
	else { $$value['id'] = get_option( $value['id'] ); }
}
?>

To fix the problem I have found that this piece of code will eliminate the errors.

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<?php
//allows the theme to get info from the theme options page
global $options;
foreach ($options as $value) {
	if ( isset( $value['id'] ) ) {
		if (get_option( $value['id'] ) === FALSE) {
			$$value['id'] = $value['std'];
		} else {
			$$value['id'] = get_option( $value['id'] );
		}
	}
}
?>

/**
* For developers: WordPress debugging mode.
*
* Change this to true to enable the display of notices during development.
* It is strongly recommended that plugin and theme developers use WP_DEBUG
* in their development environments.
*/
define('WP_DEBUG', false);

See it even tells you that this is for debugging. As advised make sure that plugin’s are deactivated. Change false to true and save the file. Upload it to the theme and any errors will be displayed where the errors are detected.  When you are finished and before you publish your theme turn the debug off.

It is also good practice to check your html (xhtml) and css with a validator service, these can be located at http://validator.w3.org/ orhttp://jigsaw.w3.org/css-validator/ respectively.