I would suggest looping through the list and use the string replace method to replace the common words that you don't care about with blanks, and then adding those to a Set of names.  And since a set does not allow for duplicates, you should end up with a list of normalized named.  

Here is some psuedo-code that should point you in the right direction.  I did not compile it or test it yet, so you will need to put it into a method, and you may need to tweak it.  Also I cannot claim credit for the toProperCase method, I found that on a different thread (https://developer.salesforce.com/forums/?id=906F00000008ukJIAQ" target="_blank).   

Hope that helps

List<String> lstAllAccountNames = new List<String>();
Set<String> setNormalizedAccountNames = new Set<String>();

// Populate the list with all your account names somehow

for(String AccountName : lstAllAccountNames){
	//Normalize to lower, and we can title-case later with a function
	String normalizedName = AccountName.toLowerCase();

	// Take out all the common words you don't care about
	// Its best to do them in an order that would make them cumlative. 
	// For example, stripping out the comma first, then the ' Inc ' allows you to get take care of 'Google, Inc' and 'Google Inc'
	// And when you later do ' Co ' you'll be covered for 'Google Co' and 'Google, Co'
	normalizedName = normalizedName.replace(', ', '');
	normalizedName = normalizedName.replace('.', '');		
	normalizedName = normalizedName.replace(' inc ', '');
	normalizedName = normalizedName.replace(' co ', '');
	normalizedName = normalizedName.replace(' ltd ', '');

	// Now convert to Title Case using another method
	normalizedName = toProperCase(normalizedName);

	// Now add it to the Set to make sure you wont' have duplicates
	setNormalizedAccountNames.add(normalizedName);
}


public static String toProperCase(String value) {
        // Normalize - Convert to lowercase
        value = value.toLowerCase();

        // Hold each word
        List<String> pieces = new List<String>();

        // Split
        for(String s : value.split(' ')) {
            // Capitalize each piece
            s = s.capitalize();

            // Add to pieces
            pieces.add(s);
        }

        // Join
        return String.join(pieces, ' ');
    }