A prototype/alpha pure PHP wrapper for the ssdeep binary (tested with version 2.4).

ExampleUsage.php

<?php
/**
 * Some examples of how to use this prototype. I highly recommend that you use
 * the PHP PECL extension I wrote instead though. It is better in every way.
 * For more information see http://php.net/ssdeep and http://pecl.php.net/ssdeep
 */

// Get a hash via a supplied file path
$SsDeep = new SsDeep();
$hash_string = $SsDeep->getHash($file);

// Find matches and near matches for a file
$matches = array();
// An array of hashes that you have previously generated and perhaps
// stored in a database as I did
$array_of_hashes = array(
	array(
		'384:fPqFB9Pg3x0bW4N6l7LTLCdLY7q4YDEhrnMm4gQJHSgY9nwE5Bhgi:6FG6bi7HOdc7q4Y4TMmiJHSgYu8j',
		'/file/name/here'
	)
));
$file = '/path/to/your/file.ext';
$SsDeep = new SsDeep();
$SsDeep->setHashes($array_of_hashes);
$matches = $SsDeep->checkMatches($file);

SsDeep.php

<?php
/**
 * I highly recommend that you use
 * the PHP PECL extension I wrote instead though. It is better in every way.
 * For more information see http://php.net/ssdeep and http://pecl.php.net/ssdeep
 *
 * @author Simon Holywell <treffynnon@php.net>
 * @version 7.5.2010 prototype
 */
class SsDeep {
	/**
	 * ssdeep hash file header format string
	 * @var string
	 */
	private $hashFileHeader = 'ssdeep,1.0--blocksize:hash:hash,filename';
	/**
	 * The temporary hash list file name
	 * @var string
	 */
	private $tempFileName = '';
	/**
	 * The contents of the hash file
	 * @var string
	 */
	private $hashes = '';

	/**
	 * Check for matches using ssdeep
	 * @param string $source_file
	 * @return boolean|array
	 */
	public function checkMatches($source_file) {
		$hashes = $this->writeHashFile();
		if($hashes) {
			$ssdeep = new SsDeepWrapper();
			$matches = $ssdeep->checkMatches($source_file, $hashes);
			$this->removeHashFile();
			return $matches;
		} else {
			return false;
		}
	}

	/**
	 * Get the hashes back in the ssdeep file format
	 * @example $this->setHashes(
	 *	array(
	 *		array(
	 *			'384:fPqFB9Pg3x0bW4N6l7LTLCdLY7q4YDEhrnMm4gQJHSgY9nwE5Bhgi:6FG6bi7HOdc7q4Y4TMmiJHSgYu8j',
	 *			'5'
	 *		)
	 *	));
	 * @param array $details
	 * @return string
	 */
	public function setHashes($details) {
		$results = array();
		$output = '';
		
		if(is_array($details)) {
			$results = $details;
		}

		foreach($results as $result) {
			$output .= $result[0] . ',"' . $result[1] . '"' . "\n";
		}
		$this->hashes = $output;
		return $output;
	}

	public function getHashes() {
		return $this->hashes;
	}

	/**
	 * Write the hashes to a temporary file
	 * @return string|boolean
	 */
	private function writeHashFile() {
		$this->tempFileName = tempnam(APPLICATION_PATH . 'temp/', '');
		$output = $this->hashFileHeader . "\n" . $this->getHashes();
		if(file_put_contents($this->tempFileName, $output)) {
			return $this->tempFileName;
		} else {
			return false;
		}
	}

	/**
	 * Delete the temporary hash list file
	 */
	private function removeHashFile() {
		if(file_exists($this->tempFileName)) {
			unlink($this->tempFileName);
		}
	}

	/**
	 * Get the hash of a file
	 * @param string $file_path
	 * @return string
	 */
	public function getHash($file_path) {
		$ssdeep = new SsDeepWrapper();
		return $ssdeep->hash($file_path);
	}
}

SsDeepWrapper.php

<?php
/**
 * I highly recommend that you use
 * the PHP PECL extension I wrote instead though. It is better in every way.
 * For more information see http://php.net/ssdeep and http://pecl.php.net/ssdeep
 *
 * @author Simon Holywell <treffynnon@php.net>
 * @version 7.5.2010 prototype
 */
class SsDeepWrapper {
	/**
	 * Location of the ssdeep binary file
	 * @var string
	 */
	private $binary = 'ssdeep';
	/**
	 * The source document to process
	 * @var string
	 */
	private $srcFileName = '/tmp/test.txt';
	/**
	 * File of hashes to compare against
	 * @var string
	 */
	private $hashListFile = '/tmp/test.txt';

	/**
	 * Calculate the hash for a given file path
	 * @param string $source_file
	 */
	public function hash($source_file = '') {
		if(!empty($source_file)) {
			$this->setSrcFileName($source_file);
		}
		$output = shell_exec($this->binary . ' -bc ' . $this->srcFileName);
		if(!preg_match('/^ssdeep,\d.\d--blocksize:hash:hash,filename\s([0-9]+:.+),".*"$/', $output, $matches)) {
			throw new SsDeepFailureException('ssdeep has failed to create a hash for the supplied file.');
		}
		return $matches[1];
	}
	/**
	 * Check for matching files already in the system.
	 * @param string $source_file
	 * @param string $hash_list
	 * @return array
	 */
	public function checkMatches($source_file = '', $hash_list = '') {
		if(!empty($source_file)) {
			$this->setSrcFileName($source_file);
		}
		if(!empty($hash_list)) {
			$this->setHashListFileName($hash_list);
		}
		exec($this->binary  . ' -bm ' . $this->hashListFile . ' ' . $this->srcFileName, $output, $return);
		$return = array();
		foreach($output as $output_line) {
			if(preg_match('/^.*\ matches\ .*:(.*)\ \((\d{1,3})\)$/', $output_line, $matches)) {
				$return[] = array(
					'filename' => $matches[1],
					'percentage' => $matches[2]
				);
			}
		}
		return $return;
	}

	/**
	 * Which file are we running this operation on?
	 * @param string $file
	 */
	public function setSrcFileName($file) {
		if(!empty($file) and
		   is_readable($file)) {
			$this->srcFileName = $file;
		} else {
			throw new SsDeepUnreadableException('The source file "' . $file . '" does not exist or is not readable.');
		}
	}

	/**
	 * Set the file with the list of hashes
	 * @param string $file
	 */
	public function setHashListFileName($file) {
		if(!empty($file) and
		   is_readable($file)) {
			$this->hashListFile = $file;
		} else {
			throw new SsDeepUnreadableException('The hash list file "' . $file . '" does not exist or is not readable.');
		}
	}
}

/**
 * Exceptions for this class
 */
class SsDeepUnreadableException extends Exception {}
class SsDeepFailureException extends Exception {}