I'm like Doomstink in that I prefer to resell the rare/high value game stuff rather than collect/hold most of it, but that mainly applies to rare/high value games I don't want or are crap. I'll pick up the uber-rare-yet-lousy games if I can get them dirt cheap simply to flip 'em, but as for my personal collection I tend to focus on collecting in other categories outside of video games - mainly film props and paraphenalia premiere party giveaways etc., comics, vintage toys, art, and weapons.
The bulk of the stuff in my video game collection is composed of the games I actually enjoy playing, but like doomstink I've had many "rare" and/or high value things pass on through and resold. Not sure which of these is the "rarest", but some of the more notable items currently in my collection/possession, off the top of my head (I know many of you have already seen these pics...eventually I will set up my game room and take new pics but for now most of my goodies are in controlled environment storage):
Earthbound complete with everything near mint/mint - found it via a craigslist ad (full story in the craigslist finds thread) along with another dozen complete/mint SNES games, some loose SNES games, an SNES "S" or 2nd version, the 2 Zelda collections on Gamecube (both sealed), and a bunch of cart only original Gameboy games, paid $140 total for everything.
This allowed me to "upgrade" my mint cart only copy, and I've gone through about a dozen or so Earthbound carts and a couple of the strategy guides that I've paid anywhere from ~$.50 (craigslist bulk game purchase of roughly 300 SNES, NES, and Genesis mostly cart only for $140) to $20 for it and resold for substantially more. One guy had 2 cart only copies of it along with a bunch of other rare/high value SNES and NES games that I paid $100 total for about 15-20 of them. Resold the carts for ~$100 a piece...I love it when one or two items in a purchase end up paying for everything (sometimes more).
Various notable complete and near mint/mint SNES games - most of these I purchased when they were originally released.
Bah just look through the
game pics - I use this photobucket account to take pics of my current notable scores (and some of the older notable ones).
Complete Virtual Boy US collection - all games complete in box, and IIRC a couple still sealed. I bought the entire collection off someone via craigslist for $100 or $120.
I've got a bunch of recent generation sealed games that are desirable - Ico (not as much anymore with the re-release), Metal Gear Solid: Twin Snakes, LoZ Collection and OoT/MQ as noted, Ninja 5-O, Shantae, Metal Gear Solid GBC, a ton more for current gen. - Metroid Trilogy etc.
Complete but opened I've got the usual suspects, most of the PS1 high demand "rarities"/high values particularly the rpgs, same with Saturn, Genesis, etc.
Various rare, obscure systems as well as some of their rare games - TurboDuo, Turbo CD, NeoGeo AES, Japanese Saturn, X'Eye...I'll have to go through the boxes most of these were bought in sets/collections and I haven't gone through them in a long time. There's no doubt other stuff but that's what I can think of and if it's really rare I've most likely sold it off.