i've been prime for >5 years now.
if you do any amount of online shopping, its SUPER easy to make that $99 fee pay for itself over the course of a year. doesnt take many 2 day shipping fee's (compared to other vendors) and you're well into the black and truly saving $$.
like all online shopping - you have to consider landed cost... that is price + shipping.
i often find that items on prime are cheaper than many company's prices without adding shipping, and i've got a couple wholesale accounts that i buy from for work that some of their products are actually more expensive than the prime price delivered once i pay for ground shipping from the wholesaler.
obviously you have to price shop, but if you're a savvy shopper - it does pay for itself easily.
one thing to watch - and this is pure 100% speculation on my part - but i *think* we're going to see a drop in the prime membership cost in the relatively near future. walmart.com is doing free 2 day shipping for all orders over $35 - in an effort to DIRECTLY compete with amazon. no membership fee required. so amazon is going to have to step up at some point or another if walmart.com starts really chipping away at their prime customer base with that. Tough to say for 100% sure, and of course you get the extra perks as a prime member (streaming video, audio, etc) besides just the free 2 day shipping.