What are the toughest thoughts to 'catch'? While meditating, it is not always clear whether you mind is clear of thoughts or not. Some seems to be more emotions or visions. But if all emotions and visions are accompanied with thoughts which are the toughest to recognize that they are there in your mind?
While BonnWarapol's five higher fetters would be the most difficult to eradicate for all non-arahants, for a beginner in meditation, the hardest to eradicate would be the five hindrances (pañca nīvaraṇāni):


Sensual desire (kāmacchanda)
Ill-will (vyāpāda)
Sloth and torpor (thīna-middha)
Restlessness and remorse (uddhacca-kukkucca)
Sceptical doubt (vicikicchā)


The commentaries by Ven. Nyanaponika Thera here or by Ven. Ajahn Brahm here, would provide more information on these. This video by Ven. Yuttadhammo Bhikkhu would also be helpful.