UGENE will allow you to annotate an alignment and highlight regions of interest (e.g., intron, UTR, gene). Most of the programs in that list posted by Gjain are for just viewing/editing an alignment. I'll bet Geneious has a really pretty set of buttons you can click to do this as well, but you'll have to buy that software.
Geneious is my favorite software for all of my bioinformatics needs, including multiple sequence alignments and annotations. It has excellent intuitive tools for adding custom annotations. It is commercial software, but academic licenses are fairly reasonably priced. The software is also cross-platform (Linux, Mac, Windows).
Next best in my opinion is CLC Genomics Workbench. This is commercial software, but many of its features can be accesed for free using "Viewer Mode". In the free viewer mode version, you can do alignments and use the standard annotations, but you cannot edit the annotations or make customized ones.
My university has a site license for DNASTAR Lasergene, but I like Geneious much better.
UGENE is free and has great potential, but it cannot wrap sequence alignments -- this makes UGENE unusable for me.