Well, if you like Spidey and Avengers, your job is probably easier than most. Let's break it down, Spidey first.
You want a good basic Spider-Man, you've got a couple of choices. On the shelves right now, you can find the new Hasbro-mold Spidey, who is fairly mediocre. Depending on where you live, you might also still have their re-release of the fabled McFarlane Spidey, with navy trim instead of light blue. He's the one that comes with a stop-light accessory. You can find him on-line for cheap if it's not on your shelves.
For black Spidey, you're probably best to wait for the new-mold Black Spidey that's on the Marvelous New home page right now. Last year's Target wave had a black Spidey who was fairly mediocre, but if you plan to buy that wave anyway to complete red Hulk, then he'll be fine.
Okay, you're on to his villains; we'll start with the Big Three. You've currently got two choices for the Green Goblin: either the Marvel Legends version, or the upcoming Hasbro version. The ML version is fine, and the unmasked variant is quite cool, but it's very "artist specific" to Romita's pencils. I find it looks less-than-intimidating, but YMMV. And, as always, if you want to build that wave's Onslaught BAF, you're probably going to want him, anyway.
The Scorpion-Venom is currently on the shelves, and while he's not as super-articulated as the older Toy Biz molds, he's certainly a fearsome-looking beast. (With the longest Venom tongue to date on a toy) The tail can be removed, if it's not to your taste. Also, the last Venom mold Toy Biz made was re-released by Hasbro (with the Mac Gargan spider design) in an earlier wave of Spidey toys. Again, if you can't find it in the stores anymore, you can still find it on-line for cheap. There's also a new, more traditional style Venom figure dud out next year; check the SDCC 2009 coverage.
The last comic-style Dr. Octopus was released as part of the Spider-Man Origins line in 2007. He was a re-release of the ML version with a darker green jumpsuit. You can still find him for cheap on-line.
You then definitely want to search for the Spider-Man: Fearsome Foes boxed set, which includes exclusive molds of Rhino, Lizard, Vulture, and a great Carnage. There's also a poor Spider-Man included.
Hasbro has also released versions of the Shocker, Tarantula, and Juggernaut in the past two years. You can also pick up Demogoblin and Mysterio from the Spider-Man Origins line for cheap (possibly on hasbro's sight, actually.) Additionally, you want to look for the Spider-Man 3 Unleashed 360 version of Sandman; it may be a movie toy, but it can pass with the comic figures, and it's generally the best Sandman ever.
Beyond that, Spider-Man villain figures tend to go for a bit cheaper on eBay than Marvel Legends from the same era. I personally recommend Hobgoblin and Jack O Lantern.
Onto the Avengers: I'll start with the Big 4: Captain America, Iron Man, Thor, and Hulk.
Captain America is easy: the Face-Off two pack. It's a great mold, and comes with the Red Skull.
Thor is a bit trickier. Which version do you want? If you just want classic Thor, the most recent edition was part of the Wal-Mart exclusive wave, so finding him would be a bit pricey. If you want the Dan Jurgans King of Asgard Thor, that was in the second wave of Hasbro Marvel Legends (Blob series), and shouldn't be too expensive. However, the cheapest Thor would be the Marvel Select modern Thor, which is readily available for retail price on-line, and may very likely be in your local comic store. Marvel Select figures aren't as articulated as MLs, but their sculpt is usually gorgeous, and Thor is a large enough character that their slightly-larger scale won't be an issue.
For Iron Man, I'm just going to go ahead and say that you want the two-pack version with Maria Hill. He's just that cool, and you get Maria Hill. And I <3 Maria Hill.
For Hulk, I'm assuming you'd just want a standard Green Savage Hulk. There are plenty of other versions of the Hulk if you want to get more specific. For him, you've got two choices: the ML Face-Off two-pack with the Leader, or the Marvel Select release from earlier this year. The Face-Off version will probably run you more, and the Select version is absolutely MASSIVE, so you might chose the latter version, particularly if you don't care for the Leader. If you get the FO version, you'll definitely want to get the ML version of Abomination, who's the same height. If you get the Select version, there's a Select Abomination and Select Thing coming out soon, who also promise to be MASSIVE. (Also, the Select Hulk is available as the Red Hulk on BBTS.com.)
Now, second-tier characters.
If you're interested in classic Avengers, Hasbro has released the following: Hercules, Quicksilver, Yellowjacket, Black Knight, Vision (Wal-Mart exclusive), Tigra (Wal-Mart exclusive), and She-Hulk. I mention the Hasbro releases because they tend to go for cheaper on-line.
If you're interested in New Avengers, you really only want the Ronin two-pack, with Electra available in normal and Skrull forms. It's still readily available on-line, if not in your local stores.
And beyond that, Toy Biz released, in roughly reverse chronological order: Wasp, Captain Marvel, both Spider-Women, Falcon, Luke Cage, Iron Fist, Wonder Man, Scarlet Witch (rare, I believe), Black Panther, War Machine, Dr. Strange, Black Widow, Hawkeye, and a Young Avengers boxed set including Hulkling, Iron Lad, Patriot, and Wiccan.
There was also a Giant Man BAF wave exclusive to Wal-Mart stores which featured Ms. Marvel and the Sentry.
For Bad Guys, Hasbro released: Crossbones (wal-Mart exclusive), Ares (Wal-Mart exclusive BAF), Absorbing Man, and a Hydra Soldier with a different-headed variant. They also recently released a Skrull Soldier/Kree Soldier two-pack, for your army building needs.
Marvel released: Baron Von Strucker in the variant Captain America face-off pack, MODOK as a BAF, Baron Zemo, Loki, Taskmaster, and Ultron.
That should be a good start.