Hey GB,
 
I consider myself being very lucky with the legendaries in this game. This is the list of my captured Legendaries in SoulSilver:
 
Entei
Raikou
Suicune
Lugia
Ho-oh
Mewtwo
 
These are the ones that I have left (As far as I know):
 
Latios
Articuno
Zapdos
Moltres
 
Im wondering if I should use my Masterball on Latios since he's a runner, and then do the save and keep going on the 3 Original Birds. Any help and oppinions are appreciated!
 
Im also looking to do a few trades with some of my pokemon, send me a private message if you are looking for something, I may have it :)

I heard Articuno is a bitch to catch

I'm sure they're all a bitch to catch.  Well use it if you'd like.  I probably would if I were in your situation.

I don't think any of the Pokemon are so difficult to catch that you need the master ball, all you need is a bit of patience.  The runners can be annoying, but there are ways to prevent them from doing so.  I'd always recommend keeping the master ball for a real emergency, like coming across a shiny Pokemon.  I know several people who found things like wild shiny Gravellers, and after the first ball failed to capture it, it exploded.  Even just trying to weaken the things can be risky.

I captured lugia with a heavy ball and only used two ultra balls previously, which I didn't find difficult at all. I think you should save it because that item is just so damn valuable in this game.
 
Also, aren't the legendaries from Sapphire and Ruby in this game too? Don't you at least get to catch Groudon?

You should usually use the Master Ball on Mewtwo.

" I don't think any of the Pokemon are so difficult to catch that you need the master ball, all you need is a bit of patience.  The runners can be annoying, but there are ways to prevent them from doing so.  I'd always recommend keeping the master ball for a real emergency, like coming across a shiny Pokemon.  I know several people who found things like wild shiny Gravellers, and after the first ball failed to capture it, it exploded.  Even just trying to weaken the things can be risky. "

most of the uncaught legendaries in that list are pretty easy to catch 
 
also, shiny's suck, they're almost pointless, and you're very unlikely to come across any unless you chain. having said that, its definately worth saving the mb

Save it...  You can trap a Liatios with Mean look or some move like that... 

Save it.

I'd use it on a ratatta, their a bitch to catch.

" @VoodooTerror: Why do they suck? All they are are rarer versions of normal Pokemon. Actually being lucky enough to come across a shiny Pokemon and catching it is very satisfying, and I'd rather be carrying a shiny around then a legendary, which takes the fun out of the game. "

shinies are great, particularly because if you even find one the pokemon is usually some random guy you would otherwise not use. The only shiny ive managed to catch ever was a shiny Tentacruel.  I wouldnt normally use a tentacruel but his shininess gave me an excuse to use an interesting pokemon i would otherwise overlook.  Of course shinies are not important if all you want to do is make a min-maxed team of ubers or crazy good ev bred guys with egg moves, but for more casual pokemon fans they are pretty great.

I'd say use it. Any stationary Pokemon are a bitch to catch, but they at least don't run away (sure, you can use a Pokemon that traps them, but they're still just as hard to catch as any other legendary). I can't really think of anything you'd have left to use it on that isn't do-able to catch with regular ole' Pokeballs (yes, Articuno took me so long I actually made a thread about it, but I tend to not even bother going after the runners since I already have them in other savegames and they're even worse to catch).

I got a shiny Spinarak.

 The legendary  birds aren't that hard to catch with patience. I can freeze Mewtwo and catch it with an Ultra Ball. The legendary  dogs are the most annoying to catch because they know Roar, but they're still catch-able after stalking them for a few hours. The other two birds aren't so bad, but a little tougher than the original legendary birds. The three Regi are the second most annoying legendary Pokemon to catch. Kyogre and Groudon aren't that bad. I never felt like getting Latias or Latios, so I just used the Master Ball on one of those out of laziness. I need the Master Ball for Rayquaza because trying to freeze it could kill it, so I just cut to the chase and use the ball. Dialga and Palkia are the easiest to get. And the other legendary ones that I didn't mention I don't care about 'cause most of the Daimond/Pearl/Platinum ones don't matter to me.

 
So yeah. Either use the Master Ball on Rayquaza (on a version where it can be found obviously), or on a shiny Pokemon that can kill its self like those son-of-a-bitch Gravellers.

Save it for a shiny, shiny Pokemon are awesome.

Wait until someone figures out an item dupe glitch. Every pokemon game has one.