Why is system shock 2 virtually impossible to buy. Its as if EA wants pple to forget it ever existed. I bought it on ebay... but that should not be the only option.
Why isnt it available on steam, gog, or even EA's game distribution site?

Given how EA have been releasing the old C&Cs completely free it's surprising that they're not doing more with the rest of their back catalogue. Maybe they're worried that they might not be easy to make compatible. But then that's why we have GOG!

I suspect the licensing involved for System Shock 2 is slightly byzantine, as it was co-developed by Irrational Games (now part of 2K) and Looking Glass Studios (now sadly defunct, but at the time they had strong ties to Eidos, who probably bought up most of their IP - and now Eidos is owned by Squeenix). So that's potentially 3 major publishers with a stake in the game, which makes things difficult.

EA retain a vice-like grip on their old IP. The only exceptions are the few they have sold. But in no cases that I know of has one of their IPs been left in uncertain legal grounds.

Why is this a surprise? Computer games have been around for over 30 years. Most titles are no longer commercially available, and likely never will be again. If you want the game, you can pay collector's prices for an existing copy, play the yard sale/ thrift store lottery , do without, or ...
It sucks but so do our current IP laws. Just be sure to support those who make our hobby possible and be scrupulous about buying what is available.

There is always the risk of backlash.
Let's take a game like Wizardry. I for one absolutely loved that series. It is my favorite dungeon craw; of all time (even prefer it to the M&M series). Now let's say that whoever owns the rights decided to re-release it. One of three things will happen:
They release it for a fee, at which point they are expected to provide support of some form. People complain because the interface is clunky (typing spells is clunky :p) and it reflects poorly upon the company ("They'll release anything for a few bucks. They killed the series, blah blah blah").
They release it for free. People still get annoyed ("They don't care about us enough to support a game. They'll just shove anything out there") and it still reflects poorly upon the company.
They release it (either way) and people like it. And it further polarizes the community ("Bah, why don't they make games like this anymore? It is so much easier to type 'mahalito' than it is to click through twelve menus or search my hotbar!").
So it is kind of a losing battle in most cases. Plus, if I recall correctly, it is kind of a bitch to get SS2 running (let alone SS1) on a modern system.
That too megacorporation-friendly for you? Try this version:
Up until a few years ago, re-releasing older games wasn't really an option. Digital distribution wasn't robust or popular enough, so the store shelf was still the main source of sales. And it costs money to get shelf space. So why waste that on an old game when you can sell more of a new one?
Then Bioshock came, which pretty dropped System Shock pretty liberally. So after that, if EA were to release SS, people would just think they were trying to take some of the shiny away from Bioshock. So it would just look like EA was grasping at straws, and it would hurt their inevitable answer to Bioshock (I think it was Spore :p).

They have GOG for both selling and supporting the game. Don't why they shouldnt. And the community itself would gladly help with support too. There's lots of community unofficial fixes and patches that make SS2 run effortlessly on modern computers. SS1 is even easier, with dosbox.

Wasn't aware SS1 worked in DOSBox. Think last time I checked it didn't.
And GoG is a fairly new service. It has only really been viable for a year or so (been around longer, but was still experimental for that first ~1 year).
And in this day and age where people get angry if something isn't patched within 30 seconds of them finding the bug, relying on the community is a bad move PR-wise.
And also, as much as I love GoG, there are reasons to not support it. GoG outright will not stock new games. Steam, Impulse, Gamersgate, and D2D WILL. And none of them like having their profits cut into. And those services will also stock old games. So unless the owner (let's assume EA for arguments sake) feels like making sure it is playable (rather than having GoG do it), it will just serve to make the other services look bad, which won't help for negotiating deals and PR on new titles (Steam will post just about anything in the news feed, but getting a promo deal with TF2 or even just getting the game mentioned on a blog will help sales a lot).

Does it make a difference? There's no shortage of those either. You still can't buy high profile classics like Ultima, Wizardry, Kings Quest, Zork, Leisure Larry, Tie Fighter, Mech Warrior 2, Flight Simulator, Sargon, M.U.L.E, Wing Commander, Populous, Civilization, Bard's Tale, Wasteland, Dungeon Master, Lemmings, Tomb Raider, etc.
Is it just me or is System Shock2 more popular today than it was 10 years ago? It seemed kind of niche at the time.

Each game is a different situation regarding the IP. Ten years ago SS2 was brand new.
SS1 works great with dosbox, being a dos title after all, and many unofficial patches make it run much better than when it was released. Of course GOG doesnt stock old games, it's on the name. I dont think i follow.

Okay. Let's say you make green widgets and red widgets. Store Alpha only sells red widgets. Stores Beta, Gamma, and Epsilon sell both green widgets and red widgets.
Stores Beta, Gamma, and Epsilon are not a fan of store Alpha since it cuts into their profit margins.
So are you going to sell Store Alpha red widgets and then sell red and green widgets to everyone else? On paper, that sounds great. Maximum profits. But lots of people make green widgets, and if Stores Beta, Gamma, and Epsilon support them, they have less competition for the red widgets.
To put it in context: Jagged Alliance 2 is STILL buggered on Steam (last I checked). Maybe that is Steam's fault, maybe it is Strategy First's. Who knows? It is NOT buggered on GoG. Can you see how that looks bad for Steam?
In other words: While you might make some decent profits reselling an old game, it isn't worth it if that hurts sales of your new ones (maybe Steam will be less willing to promote it. Maybe Impulse will only mention it in a blurb. etc)

Didn't they make the Thief series? I'm pretty sure they lost all their IP when they got shut down by their publisher, forcibly. So if it's an IP problem, Looking Glass would have nothing to say about it.
System Shock 2 was featured many times as "the best game no one bought this year". It was kind of like Sacrifice in that regard, tons of critical acclaim, few sales, large cult following after the fact.
At any rate, I guarantee whoever has it tied up is waiting to use it for some sort of promotion at some point. Maybe they will give it away for free right before Bioshock 3 or something; probably that's a dumb idea, but it will be available at some point.
It is sad you have to resort to eBay, I still have my copy, but I'm seeing more and more games become hard to get as they didn't make some sort of "retro gaming cut" needed for re-release.

Gah, my reply earlier 404'd - it's going to be a pain in the arse to repeat all of it.
Licensing is probably the biggest hurdle as far as releasing System Shock 2, and I suspect it's not only because of the publishers and developers involved.
The video files in System Shock 2 use, what was, Intel's Indeo codec. That codec was supported by Windows up until XP, and not only that, but Intel no longer own the Indeo codec. It is owned by another company who sell the codecs online for around $20US (the last I looked - you'd need to Google for information, but I think the company's name is Lingos).
When Microsoft stopped supporting the codecs in XP, even though the System Shock 2 CD has a file that installs the older version of the then Intel codecs, it tends to always fail. The only XP machine I ever got System Shock 2 to work on was a ~700Mhz Pentium 3. I believe that the only reason it worked was due to the fact that it had an integrated Intel graphics chip, and was made before XP (it was bundled with the latest and greatest OS, Millenium Edition, snicker).
The codecs are, sadly, essential. If System Shock 2 can not decode the video files it will either refuse to boot up, or boot and crash when the intro is to be played. The only way to get it working, bar other compatibility issues, is to add a command line that disables all videos. But in a story focused game, what good is that?
So on top of the scattered IP rights, there would presumably also be a licensing issue with the current owner of the codecs.
EDIT: Last sentence sounded far too definite - "there is" changed to "there would.."

I may be just incredibly lucky, but my XP computer runs SS2 without a hitch (after doing a few of the well-known and documented tricks). The videos do cause trouble every now and then, but it's not serious.
There are, if I recall correctly, three videos altogether, one of them about five seconds long and very, very unimportant. You can always play the intro before actually running the game (ffdshow seems to have no problem with the codec) and the final sequence after finishing the game and quitting to desktop - And there are no video sequences at all in the middle. Disrupting the flow of the game, sure, but not all that bad.