One shortterm apartment rental company with great locations and good prices.
http://www.easyflat2000.com/ - www.easyflat2000.com
For stays of one to three weeks, they are definitely cheaper than a hotel.

Another agency with a huge selection of apartments, but slightly higher prices:
http://www.apartmaji.si/ - http://www.apartmaji.si/

There are a few websites that list apartment rentals (among other things)
http://www.bolha.com/ - www.bolha.com
http://www.salomon.si/ - www.salomon.si
There are two challenges with most of these listings:
1. many are through agencies, that will often require a fee equal to one month's rent for their services
2. many landlords don't want to rent their flats for less than one year, or certainly not less than six months.

(depending on your budget, you might considering the cost benefits of renting a flat for 6 months, even if you only stay in it for 3 or 4. sometimes this route can be cheaper than staying in a more formal apartment through an agency.)


also some agencies
http://www.agencia.si/ - www.agencia.si
http://www.agencijabarbara.com/ - http://www.agencijabarbara.com/

you should know that the agencies usually take the equivalent of one month's rent for commission...!

look here for more english links!!
http://www.matkurja.com/en/directory/business_and_economy/real_estate/ - http://www.matkurja.com/en/directory/business_and_economy/real_estate/
http://www.matkurja.com/en/directory/business_and_economy/real_estate/real_estate_agenc... - http://www.matkurja.com/en/directory/business_and_economy/real_estate/real_estate_agenc...

I also suggest that you put a notice here:
forum_topics.asp>FID=11 - http://www.artservis.org/forum/forum_topics.asp>FID=11
I'm actually not sure how many people are reading these forums, but I'm starting to send people here when they ask me.
(NOTE: anyone reading this who has a room or flat to rent (especially for short term!) could also put a notice here...)

other tips:
Try contacting your embassy in Slovenia. Usually the embassies seem to have their own networks and contacts because there are always people coming and going. Some even have small little booklets in your native language with info about Slovenia. (not all...)

Finally, you could write a little notice and send it to anyone whom you know here in Ljubljana and ask them to send it around to their mailing list.

if you really DO want to be a tourist, there are more links for housing here:
http://www.ljubljana.si/en/accommodation/default.html - http://www.ljubljana.si/en/accommodation/default.html

good words to know to help you make sense of the websites:

nepremičnine - real estate
stanovanje - apartment
stanovanja - apartments
garsonjere - bachelor apartment (usually shared bathroom or bathroom in hallway, or one big room with kitchen and small bathroom/toilet)
enosobna - one room apartments (one room + separate kitchen + bathroom)
dvosobna - two room apartments
hiša - house
soba - room
prodam - i'm selling
oddam - i'm letting
najem - i'm renting
opremljena - furnished
najemnina - rent
dvigalo - elevator
tuš - shower
ločen tuš - separate shower
WC - toilet

hope this helps! good hunting!