Should I move to InnoDB during a planned migration?
To be honest, with a low traffic environment running on 5.1, you shouldn't have any problems with MyISAM. The biggest downfall of MyISAM is table-locking WRITES, IMO. But with limited data in the tables, this won't be noticeable.

MyISAM is probably easier to manage from a DBA standpoint with recovery and repair.

And in 5.1, I think InnoDB's benchmarks aren't really up to par. I could be wrong on this, so I'm going to look it up again!

Edit: Quick google turned up this article in 2009 using 5.1 http://www.mysqlperformanceblog.com/2009/01/12/should-you-move-from-myisam-to-innodb/

Gives some nice talking points, specifically the section on InnoDB needing tuning.

HTH