I've always used Primer3 with great success. The primers it gives you can be double-checked using the In-Silico PCR tab under the UCSC genome browser website. This will confirm that only one target will amplify. If you design primers to amplify over exon-exon junctions for expression analysis, the In-Silico PCR test should give zero results to indicate pcr failure on genomic DNA. I set my Tm's on Primer3 for 60C and run my reactions with that annealing temperature.
I use primique for designing real time PCR primers. Primer3 is also a good software. You can remove smears by loading lower amount of your real time pcr product