I've been working on this task the last few years, too, so I'd like to confirm the mention of the two working tools already mentioned — see table "Related Sanskrit Transliteration and Scansion Projects" — and also toot my own horn a bit.

My own tool "skrutable" I made so as to be able to do large tasks programmatically. For example, I just now had it analyze the meter of the Rāmāyaṇa, and it gives a full plain-text report, marking various meters and anuṣṭubh vipulās and so on, in about 20 minutes (about 15 verses per second). I've tried, but I haven't yet been able to do such things with other tools. If anyone has such experience, please let me know, I'd love to compare.

There are still a few edge-cases I need to address, and user-friendliness also needs a good bit of work. For example, the point-and-click interface is hard to get working on new machines. I plan on making a holiday project out of it, and I'll aim to send another general update after that. If anyone's especially interested, please be in touch.

Best wishes

Tyler