legendz - I hate to say this as I'd like to see SkyEurope pull through and survive or merge with another airline (it's good for competition and helps the consumer), but I would have serious concerns 7 months in advance as to whether your tickets for these 2 flights in October would be honoured.
If a vaccuum appears in the market, it is often filled pretty quickly. When Sterling who had a large base in Copenhagen ceased operations, other airlines moved in to replace them in a matter of weeks - and you will now see Cimber, Transavia and Norwegian offering many routes from Denmark. Should SkyEurope cease operations or close routes, one might see the likes of Wizzair and niki increasing the number of routes they fly from Prague and Vienna. Alternatively, Easyjet may open a Lisbon-Prague route.
It does however all depend on how important that trip is to you, and how much it would cost to buy a ticket with the likes of other airlines. You might wish to look into purchasing a ticket which is substantially (but not completely) refundable from a major airline like Lufthansa as an insurance policy - if SkyEurope are still around, you just claim the refund from Lufty, but if not you are guaranteed to be able to make your trip