I've beaten all but four of these games, here's hoping I can help.
SM64 (I think I got 25 stars)
You'll need 70 Stars to finish the game, there are a 120 total. I got 120 in 12 hours, but that's because I played it non-stop as a kid as know where to go at every turn. The way the Stars for each level are set-up means you can play it on and off until you finally get enough stars. If you want to go for 120, it's your call. I'd at least try for it on some level, but getting all those 100 coin stars will be annoying. So long as you spend some time in every world I think you're getting pretty much the full experience.
Banjo Kazoie(couldn't get through first level)
Trickier then Mario 64 in some areas, and unlike Mario 64 doesn't list which Jiggies you've done and haven't done, just how many. Also unlike Mario 64 you'll need more to get to the game's final boss fight. 94/100 Jiggies and 810/900 Music notes to reach Grunty. With that set-up it's best to commit to finding everything (or most everything) in one world at a time. Then move onto the next. Gobi's Desert and Freezy Peak need moves from each other to be finished completely, so don't agonize over them until you get all the moves. You said you couldn't get through the first level? Banjo-Kazooie doesn't work like Mario 64 where you get a Star (Jiggy in this case) and are ejected; you collect stuff until you're finished or bored, and leave. I recently speed ran the XBOX version around 9 hours, but for a first time play through, it might take you upwards of 20 hours without any guide. If it gets to overwhelming you can always skip it.
SF64
Short very fun game with great arcade gameplay. It's designed to be beaten in one sitting in around 1-2 hours. The games multiple paths and medals give it some great replay value, and you can't see every level on one play through. You'll need at least three play through to visit each level. Like Mario 64, it's a good game to play on and off. Provided you've got a decent block of time to play through it, it doesn't have a save function and the Wii's suspend feature doesn't work on N64 games. So make sure you've got some free time when you get to it.
Z:OOT(Finished 2nd dungeon)
You've got a long ways to go. If you plan to finish it I'd recommend you devote yourself to it as trying to play in-between other things might be a little confusing if your don't keep the games various rules and items fresh in your mind. Not a hard game, but a very long one, but rewarding. Tons of fun stuff to see and do, I don't recommend trying to rush through it. Make sure you're in the mood for a big adventure game when you come back around to this. 30 Hours like Noname said sounds reasonable, all though it easily could get longer depending on how much side stuff you want to do.
Rayman 2
Haven't played it, so I've got nothing on this.
Donkey Kong 64
I honestly can't remember much about DK64 despite having beaten it and collected everything, and that's kind of a bad sign, so you might take Noname's advice as possibly skip it. You free to try it, but all I remember is DK64's gameplay was kind of sluggish and clunky compared to either its 2D prequels or Mario 64 and Banjo-Kazooie. Can't remember how long it is either, but I'm guessing around Banjo-Kazooie's length.
Jet Force Gemini
Generally somewhat long, fairly challenging game with some confusing elements and goals. Big word of advice, you'll need to rescue every villager to finish the game. Also Juno is the character you must use to fight the final boss, so don't neglect powering him up. I wouldn't feel bad about skipping this one either, but try it for a while, see if you enjoy it or not.
Beyond Good and Evil(never started)
Not overly difficult adventure game and fairly reasonable playtime. It's also pretty good at keeping you on course, and if you don't obsess over getting every photo and pearl, shouldn't take you too long. Another game I don't recommend trying to play in-between playing other games. It's good though, so I'd definitely put some time in it.
Metroid Prime (or should I wait for New Play Control?)
I've never been a big fan of Metroid Prime to be honest. If you haven't started it I would wait for New Play version as that would fix one of my gripes with the game, which was sluggish combat. Anyways, the game has a built in hint system that points you in the right direction if you spend too much time going the wrong way, provided you don't turn it off. Last boss is a tad tricky, but it's pretty manageable. Length will vary depending on how lost you get, probably around 12-20 hours-ish, if you don't try to collect every last missile upgrade.
Rogue Squadron 2
Rogue Leader right? If you're just trying to finish it, not a long game, a bit tricky at times, but it's perfectly do-able. Uses a mission set-up, each with their own briefing, and the Story is just Star Wars IV-VI, so it's another decent game to play on and off. Probably take you less then 10 hours, if you try for all gold medals and the bonus missions you're looking at lot more play time. Especially the Endurance mission, which takes around a minimum of 2 1/2 hours alone.
Wind Waker
Long game, like most Zelda games. But for Wind Waker an abundance of sailing combined with a sub-par warping system introduced later in the game, and a series of somewhat tedious expensive final fetch quests across the ocean will really eat up your time. I really love Wind Waker, but it's tends to be kind of a love/hate game. It's definitely worth trying, but it's not for everybody.
Splinter Cell
I only got half-way through, got bored, and quit. So I don't have any good advice on this one.
MGS: Twin Snakes
Very VERY talky game. Tons of dialogue and cutscenes. If you find yourself enjoying the story and characters, then you probably in for good long ride. If you don't, well then skip them and enjoy a short stealth-action game. Multiple-difficulties, and not a hard game in general. Despite it's faults, it's got some pretty cool elements, the boss fights being good fun. Make sure to pay attention to Psycho Mantis. Worth playing.
Viewtiful Joe(just finished 2million leagues under the sea)
Never beat the first boss, sorry. =/
Super Mario World VC (so difficult with a GC controller)
Great game, and save function makes it good for on and off play. But if you don't have a Classic Controller, it might not be worth it. Dashing and jumping is pretty important for a lot of the game and needed to use the cape effectively. Unless you can tweak the cube controller's set-up to make it more playable, I'd skip it until you get a Classic controller.
Megaman 9(SO DIFFICULT)
Haven't played it outside the demo. Heard it's not long, just like the old games. If you want to beat it, you'll probably have to hunker down and really tear into it. Memorize everything in the level you can and stick to it. Bout all the advice I got.
Lost Winds
Short and fun adventure game. Takes about 3 hours to beat, longer if you suck. Has passive co-op as well, so you can get a friend to play with you if someone comes by. I recommend beating it in one long sitting, but it's not necessary.
Okami(I did around 5hrs)
Big ass game, like Ocarina of Time. I'd say at five hours your past the bulk of the exposition and tutorials. Like the Zelda games you should really commit your playtime to this if you want to finish it, so make sure you're in the mood for a big game when you come back to this. I think it's worth it though provided you've enjoyed what you've seen so far.
Wario Land Shake It.
Somewhat annoying, but it's not long or particularly hard game. Boss fights are kind of a pain though. Provided you're not trying for every treasure and achievement, you can beat it a reasonable amount of time. Honestly this isn't a bad game to skip either.
Zack Wiki(UP to the Mirror and the phone one)
Tricky dicky puzzle game. Good thing it's split into small bite sized pieces. How long Zack and Wiki takes depends largely on how long until you figure each puzzle. The game is set-up where you can skip some of the levels if you can't figure them out. Playing with someone else around sometimes helps and sometimes they'll spot things as a spectator you might miss as a player. (They can even use a second remote to point on the screen.) Worst case you can use the game's in-game hint system, or a guide, but i find that spoils the fun of a puzzle game. All though I will say this, one the very last level up on the control pad lets you zoom. Not sure if that'll help, but it would of saved me a lot of pain and agony. =P
Sonic Secret Rings(probably should forget about this, though I did half of them)
Not a very long game by nature, but it's tedious RPG system will drag things out. If you need advice feel free to ask for it. I wouldn't feel bad about skipping it though.
De blob(finished 2 levels)
8 more to go. Remember each level has to be finished, and there are no checkpoints or ways to suspend the game other then pausing it and leaving the Wii on. So best commit to one level at a time, and make sure you've got some free time to play it. It's a fun game, and I think it's worth it. Just take it one or two levels at a time.
Link's crossbow Training(did half of them)
You're not missing much, but if you want to try and finish it, it might take you a few hours. Somewhat longer for all Platinum medals.
And it's been long time since I played Thousand Year Door, but I remember Vivan being really useful against the Shadow Queen. Her fire was good against the hands, and her dodge move could save you a lot of damage. If all else fails, run off to do some side quests, get some better items, get up some levels.
