When I got into ponies I had a rather extensive collection of Thundercats and She-ra, including a tin She-ra trash can. The figures had all accessories/weapons and clothes including their horses and collector case. I completely and totally regret selling them. I had been bitten by the "gotta have them all" for MLP and I had just learned about the internet at the same time, so I was completely entralled by the trading and selling and buying. I have since sold most of the ponies that I had collected since I started too, so my loss of the Thundercats and She-ra honestly was for nothing in the end. I do however do not regret the many wonderful people I met along the way of my pony collecting, they all have a special place in my heart as well as the ponies that they gave to me as gifts.
As for your beanie babies, I would have to say price check ebay for lots of them and see if they are worth selling in a batch (its almost Christmas, you never know if someone is a new collector) and if that doesn't pan out, see if you can donate them to a local fire department for them to give to children of fires. I know my fire department takes in toys for that purpose, or you can check a children's hospital to see if they have a donation box.