Few things about my collection and some notes:
1. Everything's complete (including bonus stuff found in some games, especially Atlus and Working Designs games). 99% of my stuff is non-GH/PC/PH except for maybe 6 games and those have good reasoning behind them.
2. Things are generally organized alphabetically by type (complete vs sealed) and system but due to size issues with special editions and space limitations, something things are placed where they fit.
3. Some games have tags on them.
Yellow tags mean the game is missing something (either a the disc or manual) for whatever reason and therefore, is NOT part of my collection- it's only there for a reference.
Purple tags mean there's some significant issue (like a dead battery for cartridges or a crushed box) that I need to replace but these games ARE part of my collection.
4. I'm doing it over two posts, this post will show my complete collection, the next post will have my sealed collection. I do have multiples of many games so don't fret if you see doubles.
5. I took the best pictures possible but I've got a really inconsistent camera... some pictures turn out great, others don't.
6. All thumbnails should lead to a larger picture.
7. Some pictures from the big cabinet had overlap issues, so I blurred out the stuff that wasn't the focus of the picture.
Overview of the room and major storage areas.
Yeah, my room is a cramped mess. I'm running really tight on space... I had to ghetto rig a stand for some of my smaller collections.
Opened/Complete collection by system.
Playstation 3 and PSP
Notes: A few sealed games had to mixed in here due to space, such as Bayonette, Disgaea 3, Eternal Sonata, and Oblivion. Also note the 3 games with yellow tags which I traded in but kept the bonuses/extras.
[customspoiler=Highlights!]

Here we got some of the more valuable special editions, including the PAL import SE of Uncharted 2. In case you can't tell, Crisis Core is the BestBuy foil cover. [/customspoiler]
Nintendo DS
Notes: Nothing special here... but I should note, most of my DS collection will show up in the sealed section. Thanks to the R4, and now the AceKard, I never had to open any of my DS games. And no, I don't bootleg anything I don't own a legit copy of.
GameCube
Notes: Again, nothing too special... the only valuable thing here is NCAA Basketball 2K3 and the two Gamestop Exclusive RE collections.
Not picture: Mario DDR, DK Jungle Beat, and Donkey Konga 1 & 2 are all in my closet. They're too big to keep out here.
Playstation and Dreamcast
Notes: Had to take pictures of this cabinet in two halves due to all the flash glare. I think the PS1 collection is still my most valuable but due to all the PSN re-releases, it's lost a lot of value. There's still about a dozen or so games I still want to get but have put on wait due to lack of space.
BTW, Jet Grind Radio, SotN (the GH one) and Silhouette Mirage are sealed.
[customspoiler=Highlights!]

I only hand picked a few to highlight here... I've got the more valuables/rarities but it would take too long to take pictures of all of them. I've got a few DC valuables (MvCs, Power Stones, Rival Schools) but nothing too extravagant. [/customspoiler]
PC, Wii, Xbox/Xbox 360
Notes: My smaller collections are designated here. I had a lot more XB/360 games but after MS dicked me over on my third 360 repair, I got rid of most of them and picked up corresponding games on the PS2 or PS3.
Not pictured: No One Lives Forever and System Shock 2, which are in the older large-box packaging, are on my TV stand.
[customspoiler=Highlights!]

Most of these are self explanatory but the F1 2009 game is a Wii rarity for some reason... [/customspoiler]
Game Boy, GB Color, and GB Advance
Notes: My Game Boy family games. I've spent the past year and a half on these and am just about done minus a few Pokemon games. Oh, the reason why I have copies of Mega Man I & II and Link's Awakening is because one is the regular and the other is Player's Choice. I only have the PC versions because I got them real cheap and in they're in perfect shape.
[customspoiler=Highlights!]

In case you're wondering why I have two copies of all the FF games, it's because I originally had them mixed up by publisher (FF Legend III and Adventure were the Square revisions, the other two where Sunsoft). So I just decided to get both sets of each. They Square (released in the early 90s) and Sunsoft releases (released in the late 90s) are identical except the Sunsoft logo replaces the Square logo and the Sunsoft versions use the paper trays instead of plastic ones.
These are some of the most valuable games I have and a lot of their value is due to them being complete. Castlevania II and Legends easily sell for $100+ at the very least. Metroid II (including the poster) and Mega Man 3 go for $40-90. I have never seen a complete copy of Duck Tales, Gargoyle's and Mercenary Force so I don't know what their value would be. I wanted to include a few more here but decided not too because I'm lazy.

Azure Dreams is very uncommon for a complete copy- I just lucked out on a cheap copy recently. MGS and Shantae are shelf explanatory- I think Shantae is now my most valuable game (seeing these frequently go for $200+). You might be wondering why that Yu-Gi-Oh game is here... the game is worthless but the cards are very valuable. I almost sold the game and cards for $30. [customspoiler=Story.] The game, even complete, is fairly worthless. I got it in a random lot some time ago and decided to list it on eBay with a starting price of $4.99. Within 24 hours, I got a few questions and all of them had a similar topic: "are the 3 cards included?". Knowing nothing of the series, I just said yes because they were and posted the response on the listing so others could see. Then, a highly rated person offered me $30 for it and said she needed quickly for her son's B-Day. I gladly said yes and asked how she wanted it shipped so I can give her the shipping price... but then I got a bit curious about all the people asking about the cards and checked her feedback and saw that she sold a lot of Yu-Gi-Oh cards.

k Then I checked the card's values and was shocked to see them sell for $50-80 each. I emailed the lady saying I won't sell the game anymore, she cussed me out saying I ruined her son's B-Day and threatened me with a lawsuit. I told her to go ahead. Never heard from her again (and I think she got banned). [/customspoiler]

I'm guessing more and more GBA games will be valuable in the future... but for now, these are probably the best I've got. [/customspoiler]
Playstation 2 - blurred out unimportant stuff.

My single largest collection. I'm thinking of purging a lot of these due to all the HD Collections beings released.
[customspoiler=Highlights!]

Probably the few games that still hold a decent amount of value. Xenosaga III is the BestBuy lenticular cover. [/customspoiler]
SNES, NES, Saturn and Sega CD
I started in my NES collection years ago and gave up quickly. NES games are too hard to find in good, complete condition. I started on the SNES, Saturn and SegaCD Collections only within the past few months and only plan to get a few games for them (about a dozen for the SNES and Saturn, and maybe like 5 for the SegaCD). I'm having similar issues with the SNES as I did with the NES games but haven't given up yet. I've done fairly well with the Saturn and SegaCD stuff- they'll all in near mint condition (except for D).
[customspoiler=Highlights!]

All the WD games took a bit of work as I had to make sure I was getting all the stickers and whatnot. Lunacy is a really obscure game and the most uncommon game I according to DigitPress (then again, I only checked a few...).

Outside of the boxes, the internal contents of the SNES games are in fantastic shape. Oh, and Crisis Core is actually a sealed copy of the BBY foil cover... it should be included in the sealed section but I just stuck it in here since it was easier.
[/customspoiler]
Large Special Editions, Guides, Magazines, Artbooks, Lonbox PS1 games

I keep all my big special editions here- I normally keep the Artham Asylum in front of the guides, I moved it just for this picture. Peace Walker, Ar Tonelico Qoga, Atelier Rorona and Mana Khemia Alchemic Art Box are sealed. The upper shelf of guides are all PS1 guides and under those are PS2 guides. Note the Uncharted 2 Artbook, it's just the regular one, and it doesn't fit anywhere.

Bottom two shelves contain all my special edition guides. Most of these are sealed except for the doubles and the KHII, Ohimusha 3, and SoulCalibur IV guides.
The big white binder just holds smaller artbooks (usually pre-order bonuses) that I stuck in sleeves and printed some artwork for the spine. That smaller white binder has newer ones that are being collected for a second large binder.

More guides, top shelf is mixed stuff from Gamecube and a few Xbox, SNES, Sega CD/Saturn, GB/GBC guides. Second shelf is current gen consoles (Wii, PS3, 360), and the bottom shelf is GBA/PSP and small form guides (mostly DoubleJump).
I didn't bother highlighting anything on these shelves as it would take too much time. But a few note worthly items are the MGS2 Premium Package which was given out to retailers in Europe, the Xenogears Perfect Works and the BioShock artbook.
And that's all my complete stuff. Next up, the sealed stuff.