c:xampphtdocstagmorfologik>java -jar morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt
Input encoding: UTF-8
Output encoding: Cp1250
Processed 2 words in 0.003 seconds (667 words per second).

kota    kota    subst:sg:nom:f
kota    kot subst:sg:acc:m1
kota    kot subst:sg:acc:m2+subst:sg:gen:m1
kota    kot subst:sg:gen:m2

exec("java -jar C:\xampp\htdocs\tag\morfologik\morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt 2>&1 ", $result);
print_r( $result );

Array ( [0] => Nazwa 'java' nie jest rozpoznawana jako polecenie wewn�trzne lub zewn�trzne, [1] => program wykonywalny lub plik wsadowy. )
// that means somewhere about: 'java' is not recognized as internal or external command, executable or batch file

// 1)
$handle = popen("java -jar C:\xampp\htdocs\tag\morfologik\morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt 2>&1", 'r');
while(!feof($handle)) {
    $buffer = fgets($handle);
    echo "$buffer<br/>n";
    ob_flush();
    flush();
}
pclose($handle);

// 2)
echo shell_exec('java -jar C:\xampp\htdocs\tag\morfologik\morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt 2>&1 ');

// 3)
passthru("java -jar C:\xampp\htdocs\tag\morfologik\morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt 2>&1 ");

// 4)
system("java -jar C:\xampp\htdocs\tag\morfologik\morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt 2>&1 ");

java -jar C:\xampp\htdocs\tag\morfologik\morfologik-tools-1.9.0-standalone.jar plstem -i lol.txt -ie UTF-8 -o lol2.txt

c:xampphtdocstagmorfologik>cd c:

c:>java -version
java version "1.7.0_21"
Java(TM) SE Runtime Environment (build 1.7.0_21-b11)
Java HotSpot(TM) 64-Bit Server VM (build 23.21-b01, mixed mode)