This idea was suggested today so I thought I would put it down here:
When entering payments, adding the option to be able to enter in the Invoice number that you want to apply the payment to as an additional field so that it filters out all of the other Invoices. This would save time looking through a potentially very long list of invoices to apply that payment.
The same process would of course be able to be copied across to to Purchases as well.
If this is something that you'd like to see added, please remember to vote and if you have any feedback on this, please make sure to post a comment.