I am hearing what seems to be my throw out bearing and the transmission is hard to put in gear. Could it be the throw out bearing or the slave cylinder? Or the throw out bearing holder?

I'll take a stab at it. It seems as though the clutch fork is not releasing all the way and wearing out the T/O bearing. Could be the slave, but most cf these common problems lie within the bellhousing. What's the condition of the fluid? Very dark and old fluid causes common failure.
What vehicle is it?

Agree with the above posts. When was the last time you change your clutch? Try to check everything first. Then give us an update. I've also experience prob before, it was my vw clutch needs a replacement. After the said replacement, no problem encountered.. so good luck, hope you'll able to fix it soon..