GelAnalyzer finds lanes, subtracts background, finds bands with peaks, calibrates molecular weight and protein volume to standard, and adjusts for interlane differences in semiautomated fashion, and provides several visual and quantitative outputs that can be copied to other applications. It supports a limited number of input image file formats, so I used imagej to convert images to PNG before processing in gelAnalyzer. I simply didn't find this functionality in imageJ gel analysis.
PyElph is also one of best tool for gel analysis as well as dendogram construction based on molecular weight of protein or DNA fragments. Good for RFLP, PCR-RFLP, SDS-PAGE gel analysis.
PyElph, Gel Analyzer and BioNumeric (Applied Maths). PyElph is completely free and you can generate the denogram. Gel Analyzer is also free. While the BioNumeric is not free but it can be for some days.