An often asked question with no real answer. When dealing with any art, the simple answer is that it is worth whatever someone is willing to pay for it. A $50K sword that has been for sale for the past 5 years is obviously not worth $50K, and pointing out that a similar one to yours is going for that price is meaningless. Fashions and tastes change over time. There has been a drop in sword prices over the past few decades. This is possibly due to the fact that interest has increased, but so has the availability. World markets also play a major part in pricing and the economic climate currently has had a detrimental effect on items considered "luxuries" such as art.
What is true though, is that Japanese swords are a relative bargain in the world of art. Whereas a top class painting might fetch a few million $'s, a top name smith's sword can go for a mere $100K or more. A one of a kind Kiyomaru sword can fetch $300K which in terms of world art is relatively low in comparisson with other art and big names. You can also pick up a decent hand forged 500 year old blade in polish for $10K, which in terms of art is a very low price indeed.
For every good sword though, there are hundreds of mass produced swords worth a fraction of that. And because each sword is one of a kind, there is no easy price guide telling you what a sword is worth. The best way to value a sword is to look at as many swords as possible that are for sale, and to know your subject enough to be able to identify what you have.
This is all apart from the pricing on non-traditionally made military swords that do not fall in the context of art. These are militaria and values depend on prevailing market situations. Prices on these have been steadily rising to the point that you are advised to look at dealer websites to get a feel for what they are selling for. Even the machine made NCO Shin Gunto which used to sell for $300 has been selling for close to $1000 and more in excellent condition lately, so for militaria I advise you to check the current selling prices on eBay and dealer sites to gather an idea for current prices.
For traditionally made swords, it all depends on condition and other factors such as shortening, era and smith. Theoretically, all other condition, maker and workmanship factors being equal , a wakizashi would be roughly half the price of a katana, and a tanto slightly more than a wakizashi. Shinto that have been shortened are far less desirable, and Shinshinto should not be altered at all. Shortening is more accepted in Koto blades due to their age. Unsigned swords and gimei swords take a hit in price, as do the amount of flaws and staining.
Generally, the older a sword and the more important the work..the more flaws are forgiven.