My collection was far smaller than yours to start, and is far smaller than it used to be.
At it's peak, I had about 500 games across about a 12 systems.
I bought a house, and started a family, and unloaded a lot of my stuff.
Here's what I can add. Keep the stuff you are sentimental about, no matter the value. Get ready of the valuable stuff no matter how "interesting"
I'm down to about 100 games across a half dozen systems. It's still too much to play, but I kept things like:
Genesis games I got as a kid from my parents. It takes me back to my youth.
Dreamcast games I used to play with my sister and my girlfriend (now my wife).
Sega Saturn stuff that I used to save hard earned first job money.
The stuff I got rid off was the valuable things/ things I had no attachment to.
The Virtual Boy, Dragon Force on the Saturn, items that came in lots, or I though would be interesting to have.
I miss some items, but nothing terribly.
At one point I did get rid of some stuff I did love, common Genesis games, the valuable Saturn games that I did love (PDS, Guardian Heroes, Shining Force 3)
Within a month I regretted it, and had to buy them all back.
That would be my advice. Keep the things you love, get rid of the things you have. Any easy way to tell the story of the item, if it starts like "I used to play this all the time..." Keep it.
If the story is more like "I bought this item down town for way more than I should have." get rid of it.
Put a number to it if it's too hard. Aim to cut your collection by say a third, and figure out what goes.