We have friends coming to see us in Vilnius, they're flying from Germany to Stockholm on Ryanair, then by boat to Riga, and bus here. Roundtrip airfare to Stockholm for all four of them is 70 Euros, incl. tax. Might be even cheaper to catch the bus (trains aren't so great here) to Riga and then a boat to Stockholm. Also, the rumours are flying that after EU accession (May 1) the low-cost carriers are going to get into the Baltic capitals - you might want to check again after the first, to see if they'll be here in time for your trip...
Another option, low-cost carriers fly out of Prague, you might find a cheap Tallinn-Prague flight. If you're flexible about your travels, wait til you get to the Baltics - certainly the airfares available in Lithuania are a ton cheaper than any we've found on line. I'm guessing the same is true of Latvia and Estonia. We're spending August touring Latvia and Estonia, can't wait!
Weather's awesome here right now - nearly 20 degrees © and sunny. Supposed to snow on Monday, but it should be warm again and beautiful by the time you get to this part of the world. Cost of living here is waaaaaay cheaper than elsewhere in Europe, so what you may lose in transport you can easily save in accommodations and especially food.