Hi Christa-
If you post but don't get an answer in a while, send me a private message. I do not haunt this website. :-) I just check once in a while to see what's new. [Love the new stuff about online train info and about how to handle phones and ipads you take with you.]
RE antiques: Most of us trading tips here a few years back used the term "antiques" to refer to furniture shops where you could buy nice pieces, some restored, some not, in lieu of the Ikea stuff or ultra contemporary pieces otherwise so popular here. Some would also have the odd inlaid box that could be fitted with velvet to make a nice jewelry box. Some had silver or porcelain, or kitsch statues. Some of those businesses got wiped out in the 2002 flood, some got flooded again recently. I would guess you are not buying furniture, though. :-)
Off the top of my head, I am thinking you might like to poke around the antique shop at Dlouha 37, just off Revoluční in the Old Town, a short walk from the Old Town Square. It's just called Antik v Dlouhé. It has a crazy collection of all kinds of things. If you look at their website, you can decide whether you'd call them funky or not.
http://www.antik-v-dlouhe.cz/
It's in Czech, but you will learn the words for the categories of things you're looking for by looking at the photos.
I am not much for knick-knacks myself but I keep my eye out for jewelery and glass, and I am always looking for a pretty antique lamp. Some years ago, I persuaded them to sell me an art nouveau desk that they were using to display goods on. By American standards, they are very reasonably priced.
There are also small antiques at the Hotel Antik on the same street ... small selection on one side of the main entrance. A nice cafe is on the other side. I love this street for browsing. There are lots of small and interesting shops.
For Czechs, this is somewhat of a tourist area, so they'd poke around elsewhere. We have been to flea markets held Saturdays in high schools, but that takes a huge amount of time and the pickings were not so appealing. Many, many retired folks selling things to make ends meet.
If you are like me, you might enjoy poking around online before you leave. You can Google "antik" + Prague and see what you come up with. An "antikvariát" has used and old books, magazines, maybe posters, etc. If you put the whole URL in Google translate, it will usually translate the entire page. Czech declines nouns in 7 cases and the verbs are MUCH worse, so some translations are extremely approximate!!
Some of these place would be rather an adventure just to get to. See
http://www.antik-bazar.cz/kontakt.html,
the new location of one of those huge warehouse businesses that were flooded out. This is just as funky a location as the old. You would wander among the broken-down railway buildings to find it. If it's the same as it used to be, nothing is displayed or dusted. 99% certain no one there would speak English. Maybe some Russian if they were brought up under Communism or German if they choose to study it in school. My impression always was that professional antique furniture dealers from abroad got bargains and owners of funky Prague bars were in seventh heaven. Stick with shops closer to the historical center and things will be easier.
Aha, so now I have written you a whole essay. If I have time, I will adapt it as a FAQ for my website hedgie.eu. I post tips for friends and their visitors to use. These days a lot of things are covered by the official sites, so it is not so necessary, but many essentials we need to tell guests are all in one place. There's a quick, 10 minute guide to reading Czech, too. My favorite page.