It is a very good question and people have discussed and will continue to discuss this for a long time. As a general rule, there is no perfect aligner and you should aim at an alignment that that is good enough for what you want to achieve.
If you want to know more on how MultiZ, TBA and PECAN compare, here are a few comments I hope you'll find them useful. First, MultiZ is not considered a multiple alignment really as it works by simply stacking or projecting pairwise alignments to a reference species. TBA will get all the possible all-vs-all pairwise alignments and combine them into a single multiple alignment that is (I believe) refined a posteriori. I would strongly suggest you use TBA instead of MultiZ if at all possible. Pecan works similarly except that it is a global aligner and it uses the concept of consistency (tries to make the alignment between sequences A and C consistent with the alignments between A and B, and B and C) to combine all pairwise alignments into the final multiple one.
A global aligner is an aligner that will align the sequences from start to end, assuming there are no rearrangements in the sequence. When applied to whole genome sequences, it requires you to define the blocks of collinear sequences you want to align. You can use software like Enredo or Mercator for this. TBA is a local aligner and won't require this additional step.
Coming back to which software produces the best alignments, Kim and Sinha ( http://www.biomedcentral.com/1471-2105/11/54 ) showed in 2010 that PECAN outperformed other aligners (ClustalW, DIALIGN-TX, MAFFT, MAVID, MLAGAN). The same year, Chen and Tompa ( http://www.nature.com/nbt/journal/v28/n6/abs/nbt.1637.html ) used a different method to compare aligners. Again, PECAN seemed to outperform other aligners, namely MLAGAN, MAVID and TBA, especially at longer evolutionary distances (human to a non-placental mammalian species).
In short, my recommendation would be to use PECAN, but I am certainly biased (it is the aligner we use in Ensembl and I work in Ensembl). You also want to consider whether you prefer to use a local aligner like TBA that doesn't require you to pre-define the collinear blocks to be aligned or you are happy to work on getting a good homology map first. This is perfectly doable, but will require extra work.